diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py index 5b6a1730c..8bd9c72cf 100644 --- a/dpdata/abacus/md.py +++ b/dpdata/abacus/md.py @@ -1,6 +1,8 @@ +from ast import dump import os,sys import numpy as np -from .scf import ry2ev, kbar2evperang3, get_block, get_geometry_in, get_cell, get_coords +from .scf import ry2ev, bohr2ang, kbar2evperang3, get_block, get_geometry_in, get_cell, get_coords +import re # Read in geometries from an ABACUS MD trajectory. # The atomic coordinates are read in from generated files in OUT.XXXX. @@ -24,126 +26,49 @@ def get_path_out(fname, inlines): def get_coord_dump_freq(inlines): for line in inlines: - if len(line)>0 and "md_dumpmdfred" in line and "md_dumpmdfred" == line.split()[0]: + if len(line)>0 and "md_dumpfreq" in line and "md_dumpfreq" == line.split()[0]: return int(line.split()[1]) return 1 -# set up a cell according to cell info in cif file. -# maybe useful later -''' -def setup_cell(a, b, c, alpha, beta, gamma): - cell = np.zeros(3, 3) - cell[0, 0] = a - cell[1, 0] = b*np.cos(gamma/180*np.pi) - cell[1, 1] = b*np.sin(gamma/180*np.pi) - cell[2, 0] = c*np.cos(beta/180*np.pi) - cell[2, 1] = c*(b*np.cos(alpha/180*np.pi) - cell[1, 0]*np.cos(beta/180*np.pi))/cell[1, 1] - cell[2, 2] = np.sqrt(c**2 - cell[2, 0]**2 - cell[2, 1]**2) - return cell -''' - -def get_single_coord_from_cif(pos_file, atom_names, natoms, cell): - assert(len(atom_names) == len(natoms)) - nele = len(atom_names) +def get_coords_from_dump(dumplines, natoms): + nlines = len(dumplines) total_natoms = sum(natoms) - coord = np.zeros([total_natoms, 3]) - a = 0 - b = 0 - c = 0 - alpha = 0 - beta = 0 - gamma = 0 - with open(pos_file, "r") as fp: - lines = fp.read().split("\n") - for line in lines: - if "_cell_length_a" in line: - a = float(line.split()[1]) - if "_cell_length_b" in line: - b = float(line.split()[1]) - if "_cell_length_c" in line: - c = float(line.split()[1]) - if "_cell_angle_alpha" in line: - alpha = float(line.split()[1]) - if "_cell_angle_beta" in line: - beta = float(line.split()[1]) - if "_cell_angle_gamma" in line: - gamma = float(line.split()[1]) - assert(a > 0 and b > 0 and c > 0 and alpha > 0 and beta > 0 and gamma > 0) - #cell = setup_cell(a, b, c, alpha, beta, gamma) - coord_lines = get_block(lines=lines, keyword="_atom_site_fract_z", skip=0, nlines = total_natoms) - - ia_idx = 0 - for it in range(nele): - for ia in range(natoms[it]): - coord_line = coord_lines[ia_idx].split() - assert(coord_line[0] == atom_names[it]) - coord[ia_idx, 0] = float(coord_line[1]) - coord[ia_idx, 1] = float(coord_line[2]) - coord[ia_idx, 2] = float(coord_line[3]) - ia_idx+=1 - coord = np.matmul(coord, cell) - # important! Coordinates are converted to Cartesian coordinate. - return coord + nframes_dump = int(nlines/(total_natoms + 13)) - -def get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell): - total_natoms = sum(natoms) - #cell = np.zeros(ndump, 3, 3) - coords = np.zeros([ndump, total_natoms, 3]) - pos_file = os.path.join(path_out, "STRU_READIN_ADJUST.cif") - # frame 0 file is different from any other frames - coords[0] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) - for dump_idx in range(1, ndump): - pos_file = os.path.join(path_out, "md_pos_%d.cif" %(dump_idx*dump_freq)) - #print("dump_idx = %s" %dump_idx) - coords[dump_idx] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) - return coords + cells = np.zeros([nframes_dump, 3, 3]) + stresses = np.zeros([nframes_dump, 3, 3]) + forces = np.zeros([nframes_dump, total_natoms, 3]) + coords = np.zeros([nframes_dump, total_natoms, 3]) + iframe = 0 + for iline in range(nlines): + if "MDSTEP" in dumplines[iline]: + # read in LATTICE_CONSTANT + celldm = float(dumplines[iline+1].split(" ")[-1]) + # read in LATTICE_VECTORS + for ix in range(3): + cells[iframe, ix] = np.array([float(i) for i in re.split('\s+', dumplines[iline+3+ix])[-3:]]) * celldm + stresses[iframe, ix] = np.array([float(i) for i in re.split('\s+', dumplines[iline+7+ix])[-3:]]) + for iat in range(total_natoms): + coords[iframe, iat] = np.array([float(i) for i in re.split('\s+', dumplines[iline+11+iat])[-6:-3]])*celldm + forces[iframe, iat] = np.array([float(i) for i in re.split('\s+', dumplines[iline+11+iat])[-3:]]) + iframe += 1 + assert(iframe == nframes_dump) + cells *= bohr2ang + coords *= bohr2ang + stresses *= kbar2evperang3 + return coords, cells, forces, stresses -def get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names): - stress = None - total_natoms = sum(natoms) - for line in inlines: - if len(line)>0 and "stress" in line and "stress" == line.split()[0] and "1" == line.split()[1]: - stress = np.zeros([ndump, 3, 3]) - break - if type(stress) != np.ndarray: - print("The ABACUS program has no stress output. Stress will not be read.") +def get_energy(outlines, ndump, dump_freq): + energy = [] nenergy = 0 - nforce = 0 - nstress = 0 - energy = np.zeros(ndump) - force = np.zeros([ndump, total_natoms, 3]) - for line_idx, line in enumerate(outlines): if "final etot is" in line: if nenergy%dump_freq == 0: - energy[int(nenergy/dump_freq)] = float(line.split()[-2]) + energy.append(float(line.split()[-2])) nenergy+=1 - if "TOTAL-FORCE (eV/Angstrom)" in line: - for iatom in range(0, total_natoms): - force_line = outlines[line_idx+5+iatom] - atom_force = [float(i) for i in force_line.split()[1:]] - assert(len(atom_force) == 3) - atom_force = np.array(atom_force) - if nforce%dump_freq == 0: - force[int(nforce/dump_freq), iatom] = atom_force - nforce+=1 - assert(nforce==nenergy) - if "TOTAL-STRESS (KBAR)" in line: - for idx in range(0, 3): - stress_line = outlines[line_idx+4+idx] - single_stress = [float(i) for i in stress_line.split()] - if len(single_stress) != 3: - print(single_stress) - assert(len(single_stress) == 3) - single_stress = np.array(single_stress) - if nstress%dump_freq == 0: - stress[int(nstress/dump_freq), idx] = single_stress - nstress+=1 - assert(nstress==nforce) - if type(stress) == np.ndarray: - stress *= kbar2evperang3 - return energy, force, stress + assert(ndump == len(energy)) + energy = np.array(energy) + return energy def get_frame (fname): @@ -164,23 +89,27 @@ def get_frame (fname): atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) # This coords is not to be used. dump_freq = get_coord_dump_freq(inlines = inlines) - ndump = int(os.popen("ls -l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0]) + #ndump = int(os.popen("ls -l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0]) # number of dumped geometry files - coords = get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell) - - # TODO: Read in energies, forces and pressures. + #coords = get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell) + with open(os.path.join(path_out, "MD_dump"), 'r') as fp: + dumplines = fp.read().split('\n') + coords, cells, force, stress = get_coords_from_dump(dumplines, natoms) + ndump = np.shape(coords)[0] with open(os.path.join(path_out, "running_md.log"), 'r') as fp: outlines = fp.read().split('\n') - energy, force, stress = get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names) - if type(stress) == np.ndarray: - stress *= np.linalg.det(cell) + energy = get_energy(outlines, ndump, dump_freq) + for iframe in range(ndump): + stress[iframe] *= np.linalg.det(cells[iframe, :, :].reshape([3, 3])) + if np.sum(np.abs(stress[0])) < 1e-10: + stress = None data = {} data['atom_names'] = atom_names data['atom_numbs'] = natoms data['atom_types'] = types - data['cells'] = np.zeros([ndump, 3, 3]) - for idx in range(ndump): - data['cells'][:, :, :] = cell + data['cells'] = cells + #for idx in range(ndump): + # data['cells'][:, :, :] = cell data['coords'] = coords data['energies'] = energy data['forces'] = force diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py index 41dd40a70..f167c249e 100644 --- a/dpdata/abacus/scf.py +++ b/dpdata/abacus/scf.py @@ -16,15 +16,18 @@ def get_block (lines, keyword, skip = 0, nlines = None): found = True blk_idx = idx + 1 + skip line_idx = 0 - while len(lines[blk_idx]) == 0: + while len(lines[blk_idx].split("\s+")) == 0: blk_idx += 1 - while len(lines[blk_idx]) != 0 and line_idx < nlines and blk_idx != len(lines): + while line_idx < nlines and blk_idx != len(lines): + if len(lines[blk_idx].split("\s+")) == 0 or lines[blk_idx] == "": + blk_idx+=1 + continue ret.append(lines[blk_idx]) blk_idx += 1 line_idx += 1 break if not found: - raise RuntimeError("The keyword %s is not found in the script." %keyword) + return None return ret def get_geometry_in(fname, inlines): @@ -111,9 +114,11 @@ def get_energy(outlines): raise RuntimeError("Final total energy cannot be found in output. Unknown problem.") return Etot -def get_force (outlines): +def get_force (outlines, natoms): force = [] - force_inlines = get_block (outlines, "TOTAL-FORCE (eV/Angstrom)", skip = 4) + force_inlines = get_block (outlines, "TOTAL-FORCE (eV/Angstrom)", skip = 4, nlines=np.sum(natoms)) + if force_inlines is None: + raise RuntimeError("TOTAL-FORCE (eV/Angstrom) is not found in running_scf.log. Please check.") for line in force_inlines: force.append([float(f) for f in line.split()[1:4]]) force = np.array(force) @@ -121,7 +126,9 @@ def get_force (outlines): def get_stress(outlines): stress = [] - stress_inlines = get_block(outlines, "TOTAL-STRESS (KBAR)", skip = 3) + stress_inlines = get_block(outlines, "TOTAL-STRESS (KBAR)", skip = 3, nlines=3) + if stress_inlines is None: + return None for line in stress_inlines: stress.append([float(f) for f in line.split()]) stress = np.array(stress) * kbar2evperang3 @@ -151,8 +158,10 @@ def get_frame (fname): atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) energy = get_energy(outlines) - force = get_force (outlines) - stress = get_stress(outlines) * np.linalg.det(cell) + force = get_force (outlines, natoms) + stress = get_stress(outlines) + if stress is not None: + stress *= np.abs(np.linalg.det(cell)) data = {} data['atom_names'] = atom_names @@ -162,7 +171,8 @@ def get_frame (fname): data['coords'] = coords[np.newaxis, :, :] data['energies'] = np.array(energy)[np.newaxis] data['forces'] = force[np.newaxis, :, :] - data['virials'] = stress[np.newaxis, :, :] + if stress is not None: + data['virials'] = stress[np.newaxis, :, :] data['orig'] = np.zeros(3) # print("atom_names = ", data['atom_names']) # print("natoms = ", data['atom_numbs']) diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py index 43403772a..aec05a7db 100644 --- a/dpdata/plugins/abacus.py +++ b/dpdata/plugins/abacus.py @@ -5,6 +5,7 @@ @Format.register("abacus/scf") @Format.register("abacus/pw/scf") +@Format.register("abacus/lcao/scf") class AbacusSCFFormat(Format): #@Format.post("rot_lower_triangular") def from_labeled_system(self, file_name, **kwargs): diff --git a/dpdata/qe/scf.py b/dpdata/qe/scf.py index 48f618a96..50312aee3 100755 --- a/dpdata/qe/scf.py +++ b/dpdata/qe/scf.py @@ -70,7 +70,7 @@ def get_coords (lines, cell) : coord.append([float(jj) for jj in ii.split()[1:4]]) atom_symbol_list.append(ii.split()[0]) coord = np.array(coord) - coord = np.matmul(coord, cell.T) + coord = np.matmul(coord, cell) atom_symbol_list = np.array(atom_symbol_list) tmp_names, symbol_idx = np.unique(atom_symbol_list, return_index=True) atom_types = [] diff --git a/tests/abacus.md/INPUT b/tests/abacus.md/INPUT index d169ddf95..5986c0ba5 100644 --- a/tests/abacus.md/INPUT +++ b/tests/abacus.md/INPUT @@ -1,30 +1,43 @@ INPUT_PARAMETERS -#Parameters (General) -suffix autotest -pseudo_dir ./ -ntype 1 -nbands 8 -calculation md -read_file_dir ./ +#Parameters (1.General) +suffix abacus +calculation md +ntype 2 +nbands 6 +symmetry 0 -#Parameters (Accuracy) -ecutwfc 20 -niter 20 +#Parameters (2.Iteration) +ecutwfc 50 +scf_thr 1e-2 +scf_nmax 50 -basis_type pw -nstep 21 # number of MD/relaxation steps +#Parameters (3.Basis) +basis_type lcao +gamma_only 1 -stress 1 -stress_thr 1e-6 -force 1 -force_thr_ev 1.0e-3 +#Parameters (4.Smearing) +smearing_method gaussian +smearing_sigma 0.02 -ks_solver cg -mixing_type pulay -mixing_beta 0.7 +#Parameters (5.Mixing) +mixing_type pulay +mixing_beta 0.4 -md_mdtype 1 # 0 for NVE; 1 for NVT with Nose Hoover; 2 for NVT with velocity rescaling -md_tfirst 10 # temperature, unit: K -md_dt 1 # unit: fs -md_rstmd 0 # 1 for restart -md_dumpmdfred 5 +#Parameters (6.Deepks) +#cal_force 1 +#test_force 1 +#deepks_out_labels 1 +#deepks_descriptor_lmax 2 +#deepks_scf 1 +#deepks_model model.ptg + +md_type 1 +md_dt 0.1 +md_tfirst 300 +md_tfreq 0.1 +md_restart 0 +md_dumpfreq 5 +md_nstep 20 +out_level m + +cal_stress 1 diff --git a/tests/abacus.md/OUT.abacus/MD_dump b/tests/abacus.md/OUT.abacus/MD_dump new file mode 100644 index 000000000..f35852368 --- /dev/null +++ b/tests/abacus.md/OUT.abacus/MD_dump @@ -0,0 +1,80 @@ +MDSTEP: 0 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + 0.342473709368 -0.250611694353 -0.053956446640 + -0.250611694353 0.199085269192 -0.098626841062 + -0.053956446640 -0.098626841062 0.476228570252 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 15.953212941138 18.765586146743 8.395247471322 0.863308639441 -0.443254999104 -0.756985212833 + 1 H 13.771131204099 20.615493002741 7.611989524536 -0.200930881908 0.468126173231 -1.160958093908 + 2 O 14.513210882571 19.684192208442 8.958321352729 -0.662377757533 -0.024871174127 1.917943306741 + + +MDSTEP: 5 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + 0.154743825476 -0.125714918816 0.000149755944 + -0.125714918816 0.119479071004 -0.140313773379 + 0.000149755944 -0.140313773379 0.457169606881 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 15.972712462196 18.750422243865 8.413062924828 0.308447002711 -0.100596917061 -0.518349474860 + 1 H 13.786987486168 20.622823511243 7.605308823456 -0.219930471300 0.466062785475 -1.095536719299 + 2 O 14.510983383443 19.684685730795 8.957619837020 -0.088516531411 -0.365465868414 1.613886194160 + + +MDSTEP: 10 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + -0.091192063445 0.052076615726 0.020742614517 + 0.052076615726 -0.012621430602 -0.137196630015 + 0.020742614517 -0.137196630015 0.376312058179 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 15.993574661987 18.734845521277 8.428473898762 -0.421531963990 0.478003484039 -0.602669270783 + 1 H 13.801966849306 20.632160064055 7.593719582169 0.265214977762 0.076407086378 -0.963824371968 + 2 O 14.508725280299 19.685078876234 8.957379058834 0.156316986228 -0.554410570417 1.566493642751 + + +MDSTEP: 15 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + -0.247917742642 0.164910534300 0.034034337680 + 0.164910534300 -0.098300168752 -0.128317310754 + 0.034034337680 -0.128317310754 0.301502887031 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 16.013474681966 18.720459436062 8.442030452618 -0.543198631066 0.457161183663 -0.206821526696 + 1 H 13.816825157151 20.642826422172 7.577781781099 0.022709639914 0.211549051866 -0.758980258266 + 2 O 14.506535423527 19.685313227829 8.957529083034 0.520488991152 -0.668710235529 0.965801784963 + + +MDSTEP: 20 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + -0.404277528792 0.286670843238 0.018904177312 + 0.286670843238 -0.202681869786 -0.083866196906 + 0.018904177312 -0.083866196906 0.189108946079 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 16.030788395118 18.708219053395 8.454627488439 -0.812329959008 0.587918500063 0.000941318509 + 1 H 13.831803451625 20.654370023278 7.558509583331 0.039826431878 0.100785737160 -0.450166047811 + 2 O 14.504500950754 19.685357126714 8.957949634007 0.772503527130 -0.688704237222 0.449224729302 + + diff --git a/tests/abacus.md/OUT.abacus/running_md.log b/tests/abacus.md/OUT.abacus/running_md.log new file mode 100644 index 000000000..c099ca4da --- /dev/null +++ b/tests/abacus.md/OUT.abacus/running_md.log @@ -0,0 +1,2284 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Apr 13 14:58:14 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.abacus/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = H + atom label for species 2 = O + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_H1 15.9532129411 18.7655861467 8.39524747132 0 0 0 0 + tauc_H2 13.7711312041 20.6154930027 7.61198952454 0 0 0 0 + tauc_O1 14.5132108826 19.6841922084 8.95832135273 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: H_gga_8au_60Ry_2s1p.orb + orbital file: O_gga_7au_60Ry_2s2p1d.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 +0 +0 + +0 +0.0357142857143 +0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + SETUP THE ELECTRONS NUMBER + electron number of element H = 1 + total electron number of element H = 2 + electron number of element O = 6 + total electron number of element O = 6 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 6 + NBANDS = 6 + DONE : SETUP UNITCELL Time : 0.0345590766519 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0349359968677 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3118 262044 + 3 3117 262043 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(W) PW + 1 3117 262043 + 2 3118 262044 + 3 3117 262043 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + + SETUP COORDINATES OF PLANE WAVES + number of total plane waves = 1048171 + + SETUP COORDINATES OF PLANE WAVES + number of |g| = 3309 + max |g| = 5.06505102041 + min |g| = 0 + DONE : INIT PLANEWAVE Time : 1.2043611249 (SEC) + + DONE : INIT CHARGE Time : 1.25489114318 (SEC) + + DONE : INIT POTENTIAL Time : 1.26592466421 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 801 0.01 8 1 1 + 2 0 1 801 0.01 8 1 1 + 3 1 0 801 0.01 8 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 701 0.01 7 1 1 + 2 0 1 701 0.01 7 1 1 + 3 1 0 701 0.01 7 1 1 + 4 1 1 701 0.01 7 1 1 + 5 2 0 701 0.01 7 1 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + init_chg = atomic + nloc = 144 + searching radius is (Bohr)) = 16.01 + searching radius unit is (Bohr)) = 1 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 436 ; sender_size of each process is: +144 144 144 4 + gamma_only_local = 1 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 436 + sender_size = 436 + last sender_buffer = 0.000987248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000213871 + + Density error is 0.22907025181 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 2 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 436 + sender_size = 436 + last sender_buffer = 0.00124178 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000232881 + + Density error is 0.0983063523487 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 3 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 436 + sender_size = 436 + last sender_buffer = 0.00119187 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00023854 + + Density error is 0.0630382071563 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 4 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 436 + sender_size = 436 + last sender_buffer = 0.00111123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000247594 + + Density error is 0.00212188907864 + + charge density convergence is achieved + final etot is -466.692851174 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.86330858 -0.44325497 -0.75698516 + H2 -0.20093087 +0.46812614 -1.160958 + O1 -0.66237771 -0.024871173 +1.9179432 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.342474 -0.250612 -0.053956 + -0.250612 +0.199085 -0.098627 + -0.053956 -0.098627 +0.476229 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 0 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is +0.364728 Kbar +Virial Term is +0.339263 Kbar +Kenetic Term is +0.025466 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.381046 -0.260771 -0.035926 + -0.260771 +0.213637 -0.116654 + -0.035926 -0.116654 +0.499502 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 2 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001111 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000246 + + Density error is +0.000812965099 + + charge density convergence is achieved + final etot is -466.694119113669 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.64655531 -0.33147708 -0.63237758 + H2 -0.27582922 +0.48531937 -1.07451897 + O1 -0.37072609 -0.15384229 +1.70689655 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.304825 -0.225915 -0.041597 + -0.225915 +0.184120 -0.109536 + -0.041597 -0.109536 +0.476180 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 3 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001109 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000249 + + Density error is +0.000712200370 + + charge density convergence is achieved + final etot is -466.695421284274 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.61896149 -0.29339215 -0.65503589 + H2 -0.21205075 +0.46474918 -1.12721978 + O1 -0.40691074 -0.17135703 +1.78225568 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.270131 -0.203129 -0.030432 + -0.203129 +0.169841 -0.118202 + -0.030432 -0.118202 +0.473338 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001106 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000249 + + Density error is +0.000693457887 + + charge density convergence is achieved + final etot is -466.696750196281 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.48644933 -0.21743108 -0.58788434 + H2 -0.24325232 +0.47926564 -1.10488732 + O1 -0.24319701 -0.26183455 +1.69277166 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.232348 -0.178143 -0.019038 + -0.178143 +0.154110 -0.127129 + -0.019038 -0.127129 +0.469916 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 5 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001105 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000251 + + Density error is +0.000831214560 + + charge density convergence is achieved + final etot is -466.698028090263 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.40250864 -0.15283133 -0.57921295 + H2 -0.19163250 +0.44793586 -1.10996658 + O1 -0.21087614 -0.29510452 +1.68917953 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.192212 -0.150822 -0.009745 + -0.150822 +0.135827 -0.133329 + -0.009745 -0.133329 +0.463055 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 6 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001101 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000252 + + Density error is +0.000741826297 + + charge density convergence is achieved + final etot is -466.699290513689 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.30844698 -0.10059691 -0.51834944 + H2 -0.21993046 +0.46606276 -1.09553665 + O1 -0.08851653 -0.36546584 +1.61388609 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.154744 -0.125715 +0.000150 + -0.125715 +0.119479 -0.140314 + +0.000150 -0.140314 +0.457170 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 5 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is +0.270990 Kbar +Virial Term is +0.243798 Kbar +Kenetic Term is +0.027192 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.197322 -0.137704 +0.012493 + -0.137704 +0.137750 -0.159772 + +0.012493 -0.159772 +0.477896 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 7 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001100 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000254 + + Density error is +0.001296852096 + + charge density convergence is achieved + final etot is -466.700352492361 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.18090284 -0.00124347 -0.52452226 + H2 -0.13733836 +0.40367906 -1.08114493 + O1 -0.04356447 -0.40243559 +1.60566719 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.108237 -0.092885 +0.006743 + -0.092885 +0.096063 -0.142871 + +0.006743 -0.142871 +0.444942 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 8 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001095 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000255 + + Density error is +0.001373100441 + + charge density convergence is achieved + final etot is -466.701391168881 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.14255182 -0.00101230 -0.42624709 + H2 -0.21850033 +0.46069015 -1.06078607 + O1 +0.07594851 -0.45967785 +1.48703316 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.076272 -0.071788 +0.016002 + -0.071788 +0.082562 -0.149268 + +0.016002 -0.149268 +0.438978 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 9 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001096 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000256 + + Density error is +0.002916062746 + + charge density convergence is achieved + final etot is -466.701752940586 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.07047054 +0.18417814 -0.50830181 + H2 -0.02028818 +0.30684812 -1.03356989 + O1 +0.09075872 -0.49102625 +1.54187171 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.016733 -0.027790 +0.017836 + -0.027790 +0.048898 -0.145410 + +0.017836 -0.145410 +0.417656 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 10 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001086 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000258 + + Density error is +0.004281856614 + + charge density convergence is achieved + final etot is -466.701784879168 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.03821444 +0.03386400 -0.27622989 + H2 -0.29847686 +0.50989617 -1.00686614 + O1 +0.26026241 -0.54376017 +1.28309603 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.005309 -0.022976 +0.029731 + -0.022976 +0.048804 -0.155863 + +0.029731 -0.155863 +0.418836 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 11 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001095 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000259 + + Density error is +0.008284286772 + + charge density convergence is achieved + final etot is -466.698298260896 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.42153194 +0.47800345 -0.60266923 + H2 +0.26521496 +0.07640708 -0.96382431 + O1 +0.15631698 -0.55441053 +1.56649354 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.091192 +0.052077 +0.020743 + +0.052077 -0.012621 -0.137197 + +0.020743 -0.137197 +0.376312 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 10 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is +0.118981 Kbar +Virial Term is +0.090833 Kbar +Kenetic Term is +0.028148 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.049247 +0.041841 +0.026216 + +0.041841 +0.006782 -0.157984 + +0.026216 -0.157984 +0.399408 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 12 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001068 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000260 + + Density error is +0.013857092147 + + LCAO ALGORITHM ------------- MD = 12 ELEC = 2 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001085 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000261 + + Density error is +0.001589448966 + + charge density convergence is achieved + final etot is -466.703909676999 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.28674705 +0.32257779 -0.39663257 + H2 +0.02955609 +0.25720918 -0.94465129 + O1 +0.25719096 -0.57978697 +1.34128386 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.102767 +0.057764 +0.030039 + +0.057764 -0.014383 -0.144341 + +0.030039 -0.144341 +0.373965 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 13 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001077 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000262 + + Density error is +0.002070240779 + + charge density convergence is achieved + final etot is -466.704036345606 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.32428699 +0.29359387 -0.24641838 + H2 -0.12773856 +0.34751550 -0.88532823 + O1 +0.45202555 -0.64110937 +1.13174660 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.129688 +0.076052 +0.035709 + +0.076052 -0.026981 -0.146605 + +0.035709 -0.146605 +0.363477 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 14 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001080 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000264 + + Density error is +0.004359931704 + + charge density convergence is achieved + final etot is -466.702852817573 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.55904989 +0.52796169 -0.41105586 + H2 +0.19505420 +0.09971169 -0.84000299 + O1 +0.36399569 -0.62767338 +1.25105885 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.195852 +0.127521 +0.029560 + +0.127521 -0.069558 -0.132591 + +0.029560 -0.132591 +0.330830 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 15 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001065 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000265 + + Density error is +0.006891676295 + + charge density convergence is achieved + final etot is -466.700543051512 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.34568768 +0.25462803 -0.05926056 + H2 -0.26550846 +0.43144795 -0.80103265 + O1 +0.61119614 -0.68607598 +0.86029320 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.187581 +0.117448 +0.041239 + +0.117448 -0.058254 -0.143489 + +0.041239 -0.143489 +0.334349 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 16 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001081 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000268 + + Density error is +0.013146435036 + + LCAO ALGORITHM ------------- MD = 16 ELEC = 2 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001066 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000268 + + Density error is +0.001586984246 + + charge density convergence is achieved + final etot is -466.703646638347 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.54319860 +0.45716115 -0.20682151 + H2 +0.02270964 +0.21154904 -0.75898021 + O1 +0.52048896 -0.66871019 +0.96580172 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.247918 +0.164911 +0.034034 + +0.164911 -0.098300 -0.128317 + +0.034034 -0.128317 +0.301503 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 15 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is +0.012883 Kbar +Virial Term is -0.014905 Kbar +Kenetic Term is +0.027788 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.210636 +0.159462 +0.032546 + +0.159462 -0.080357 -0.150043 + +0.032546 -0.150043 +0.329644 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 17 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001067 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000269 + + Density error is +0.003632561369 + + charge density convergence is achieved + final etot is -466.702235890628 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.80094970 +0.67278361 -0.30718791 + H2 +0.24366564 +0.00932187 -0.67175682 + O1 +0.55728406 -0.68210548 +0.97894473 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.307521 +0.211953 +0.026554 + +0.211953 -0.138106 -0.113019 + +0.026554 -0.113019 +0.268271 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 18 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001054 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000271 + + Density error is +0.005595449442 + + charge density convergence is achieved + final etot is -466.700163595798 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.59763214 +0.43904849 -0.03472448 + H2 -0.09248416 +0.25763720 -0.63673302 + O1 +0.69011630 -0.69668569 +0.67145750 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.303840 +0.206886 +0.033204 + +0.206886 -0.132651 -0.117370 + +0.033204 -0.117370 +0.264195 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 19 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001066 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000273 + + Density error is +0.010881139789 + + LCAO ALGORITHM ------------- MD = 19 ELEC = 2 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001054 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000273 + + Density error is +0.001371997750 + + charge density convergence is achieved + final etot is -466.701537327762 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.77301593 +0.61134487 -0.14930516 + H2 +0.13253222 +0.07664781 -0.58340174 + O1 +0.64048370 -0.68799268 +0.73270691 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.355835 +0.248594 +0.024707 + +0.248594 -0.169021 -0.100853 + +0.024707 -0.100853 +0.231354 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 20 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001054 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000275 + + Density error is +0.003244323553 + + charge density convergence is achieved + final etot is -466.699800890155 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.98747030 +0.79286130 -0.23966801 + H2 +0.33571389 -0.11433771 -0.49025776 + O1 +0.65175640 -0.67852359 +0.72992577 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.407715 +0.290577 +0.015274 + +0.290577 -0.205965 -0.083362 + +0.015274 -0.083362 +0.197294 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 21 ELEC = 1 -------------------------------- + +temp variables are deleted + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +436 + sender_size = +436 + last sender_buffer = +0.001042 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000277 + + Density error is +0.004953382147 + + charge density convergence is achieved + final etot is -466.697608297566 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.81232991 +0.58791846 +0.00094132 + H2 +0.03982643 +0.10078573 -0.45016602 + O1 +0.77250348 -0.68870419 +0.44922470 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.404278 +0.286671 +0.018904 + +0.286671 -0.202682 -0.083866 + +0.018904 -0.083866 +0.189109 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 20 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is -0.113167 Kbar +Virial Term is -0.139283 Kbar +Kenetic Term is +0.026116 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.373570 +0.287440 +0.010819 + +0.287440 -0.188168 -0.105266 + +0.010819 -0.105266 +0.222236 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.6976082975657505 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total +132.35550 11 +12.03 +100.00% + Run_lcao lcao_line +132.33977 1 +132.34 +99.99% + PW_Basis gen_pw +1.16916 1 +1.17 +0.88% + PW_complement get_total_pw +0.11398 10 +0.01 +0.09% + PW_complement setup_GVectors +0.25635 10 +0.03 +0.19% + mymath heapsort +0.20875 10 +0.02 +0.16% + PW_Basis setup_struc_factor +0.47204 21 +0.02 +0.36% + ORB_control read_orb_first +0.12504 1 +0.13 +0.09% + LCAO_Orbitals Read_Orbitals +0.12504 1 +0.13 +0.09% + ORB_control set_orb_tables +1.21148 1 +1.21 +0.92% + ORB_gen_tables gen_tables +1.21148 1 +1.21 +0.92% + ORB_table_phi init_Table +0.71243 1 +0.71 +0.54% + ORB_table_phi cal_ST_Phi12_R +0.70420 126 +0.01 +0.53% + ORB_table_beta init_Table_Beta +0.30461 1 +0.30 +0.23% + ORB_table_beta VNL_PhiBeta_R +0.30229 56 +0.01 +0.23% + Potential init_pot +24.59861 42 +0.59 +18.59% + Potential set_local_pot +1.80187 42 +0.04 +1.36% + FFT FFT3D +39.89220 1316 +0.03 +30.14% + Charge atomic_rho +3.11639 41 +0.08 +2.35% + Potential v_of_rho +36.45681 69 +0.53 +27.54% + XC_Functional v_xc +39.40750 90 +0.44 +29.77% + H_Hartree_pw v_hartree +5.69526 69 +0.08 +4.30% + Potential set_vr_eff +0.22940 69 +0.00 +0.17% + Run_MD_LCAO opt_ions +128.93060 1 +128.93 +97.41% + NVT_NHC setup +8.70219 1 +8.70 +6.57% + MD_func force_stress +63.15373 11 +5.74 +47.72% + LOOP_elec solve_elec_stru +30.69312 21 +1.46 +23.19% + LOOP_elec set_matrix_grid +1.76637 21 +0.08 +1.33% + Grid_Technique init +1.76335 21 +0.08 +1.33% + Grid_BigCellgrid_expansion_index +1.39932 42 +0.03 +1.06% + LOOP_elec solver +28.90742 21 +1.38 +21.84% + ELEC_scf scf +28.90729 21 +1.38 +21.84% + H_Ewald_pw compute_ewald +0.21927 21 +0.01 +0.17% + ELEC_cband_gamma cal_bands +5.01029 27 +0.19 +3.79% + LCAO_Hamilt cal_Hgamma +4.88214 27 +0.18 +3.69% + Gint_Gamma cal_vlocal +4.88196 27 +0.18 +3.69% + Gint_Gamma gamma_vlocal +3.34387 27 +0.12 +2.53% + Local_Orbital_Cha sum_bands +6.29288 27 +0.23 +4.75% + Gint_Gamma cal_rho +6.22736 27 +0.23 +4.71% + Gint_Gamma gamma_charge +6.22723 27 +0.23 +4.70% + Gint_Gamma reduce_charge +1.93070 27 +0.07 +1.46% + Charge mix_rho +2.62751 27 +0.10 +1.99% + Force_Stress_LCAO getForceStress +82.70782 21 +3.94 +62.49% + Forces cal_force_loc +1.64530 21 +0.08 +1.24% + Forces cal_force_ew +0.76779 21 +0.04 +0.58% + Stress_Func stress_loc +2.86125 21 +0.14 +2.16% + Stress_Func stress_har +2.01964 21 +0.10 +1.53% + Stress_Func stress_ew +1.07900 21 +0.05 +0.82% + Stress_Func stress_gga +4.78231 21 +0.23 +3.61% + Force_LCAO_gamma ftable_gamma +56.46509 21 +2.69 +42.66% + Force_LCAO_gamma cal_fvl_dphi +56.40976 21 +2.69 +42.62% + Gint_Gamma cal_force +44.33796 21 +2.11 +33.50% + Gint_Gamma gamma_force +26.79047 21 +1.28 +20.24% + Gint_Gamma gamma_force_wait +17.53623 21 +0.84 +13.25% + MD_func md_force_stress +60.66036 11 +5.51 +45.83% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + +1374.8320 + ORB_table_phi Jl(x) +97.8037 + Charge_Pulay Rrho +32.0000 + Charge_Pulay dRrho +28.0000 + Charge_Pulay drho +28.0000 + Use_FFT porter +8.0000 + PW_Basis struc_fac +7.9969 + Grid_Meshcell index2normal +4.1684 + Grid_Meshcell index2ucell +4.1684 + Charge rho +4.0000 + Charge rho_save +4.0000 + Charge rho_core +4.0000 + Potential vltot +4.0000 + Potential vr +4.0000 + Potential vr_eff +4.0000 + Potential vr_eff1 +4.0000 + Potential vnew +4.0000 + Charge_Pulay rho_save2 +4.0000 + ORB_table_phi Table_SR&TR +3.2158 + Charge rhog +1.9992 + Charge rhog_save +1.9992 + Charge kin_r +1.9992 + Charge kin_r_save +1.9992 + Charge rhog_core +1.9992 + ORB_table_beta Table_NR +1.0437 + ---------------------------------------------------------- + + Start Time : Wed Apr 13 14:58:14 2022 + Finish Time : Wed Apr 13 15:00:27 2022 + Total Time : 0 h 2 mins 13 secs diff --git a/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif b/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif deleted file mode 100644 index 24779f6c0..000000000 --- a/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0 0 0 -Si 0.245 0.237 0.265 diff --git a/tests/abacus.md/OUT.autotest/md_pos_1.cif b/tests/abacus.md/OUT.autotest/md_pos_1.cif deleted file mode 100644 index 832aaef0a..000000000 --- a/tests/abacus.md/OUT.autotest/md_pos_1.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.00106888 0.99849 0.000247409 -Si 0.245535 0.237394 0.262886 diff --git a/tests/abacus.md/OUT.autotest/md_pos_10.cif b/tests/abacus.md/OUT.autotest/md_pos_10.cif deleted file mode 100644 index a7546cea6..000000000 --- a/tests/abacus.md/OUT.autotest/md_pos_10.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.00711478 0.993904 0.9916 -Si 0.253316 0.23197 0.255312 diff --git a/tests/abacus.md/OUT.autotest/md_pos_15.cif b/tests/abacus.md/OUT.autotest/md_pos_15.cif deleted file mode 100644 index 51f15b4ea..000000000 --- a/tests/abacus.md/OUT.autotest/md_pos_15.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.00722617 0.979891 0.000667301 -Si 0.260608 0.240666 0.237553 diff --git a/tests/abacus.md/OUT.autotest/md_pos_20.cif b/tests/abacus.md/OUT.autotest/md_pos_20.cif deleted file mode 100644 index 3d01862a9..000000000 --- a/tests/abacus.md/OUT.autotest/md_pos_20.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.0136053 0.987589 0.984304 -Si 0.261345 0.227707 0.245529 diff --git a/tests/abacus.md/OUT.autotest/md_pos_5.cif b/tests/abacus.md/OUT.autotest/md_pos_5.cif deleted file mode 100644 index b35b1102d..000000000 --- a/tests/abacus.md/OUT.autotest/md_pos_5.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.999048 0.984501 0.010401 -Si 0.2538 0.246892 0.24541 diff --git a/tests/abacus.md/OUT.autotest/running_md.log b/tests/abacus.md/OUT.autotest/running_md.log deleted file mode 100644 index 16f460507..000000000 --- a/tests/abacus.md/OUT.autotest/running_md.log +++ /dev/null @@ -1,2608 +0,0 @@ - - WELCOME TO ABACUS - - 'Atomic-orbital Based Ab-initio Computation at UStc' - - Website: http://abacus.ustc.edu.cn/ - - Version: Parallel, in development - Processor Number is 1 - Start Time is Fri Oct 15 14:37:16 2021 - - ------------------------------------------------------------------------------------ - - READING GENERAL INFORMATION - global_out_dir = OUT.autotest/ - global_in_card = INPUT - pseudo_dir = ./ - orbital_dir = ./ - pseudo_type = auto - DRANK = 1 - DSIZE = 1 - DCOLOR = 1 - GRANK = 1 - GSIZE = 1 - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | Reading atom information in unitcell: | - | From the input file and the structure file we know the number of | - | different elments in this unitcell, then we list the detail | - | information for each element, especially the zeta and polar atomic | - | orbital number for each element. The total atom number is counted. | - | We calculate the nearest atom distance for each atom and show the | - | Cartesian and Direct coordinates for each atom. We list the file | - | address for atomic orbitals. The volume and the lattice vectors | - | in real and reciprocal space is also shown. | - | | - <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - - - - READING UNITCELL INFORMATION - ntype = 1 - atom label for species 1 = Si - lattice constant (Bohr) = 10.2 - lattice constant (Angstrom) = 5.39761 - - READING ATOM TYPE 1 - atom label = Si - L=0, number of zeta = 1 - L=1, number of zeta = 1 - L=2, number of zeta = 1 - number of atom for this type = 2 - start magnetization = FALSE - start magnetization = FALSE - - TOTAL ATOM NUMBER = 2 - - CARTESIAN COORDINATES ( UNIT = 10.2 Bohr ). - atom x y z mag vx vy vz - tauc_Si1 0 0 0 0 0 0 0 - tauc_Si2 0.241 0.255 0.250999999999 0 0 0 0 - - - Volume (Bohr^3) = 265.302 - Volume (A^3) = 39.3136533177 - - Lattice vectors: (Cartesian coordinate: in unit of a_0) - +0.5 +0.5 +0 - +0.5 +0 +0.5 - +0 +0.5 +0.5 - Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) - +1 +1 -1 - +1 -1 +1 - -1 +1 +1 - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | Reading pseudopotentials files: | - | The pseudopotential file is in UPF format. The 'NC' indicates that | - | the type of pseudopotential is 'norm conserving'. Functional of | - | exchange and correlation is decided by 4 given parameters in UPF | - | file. We also read in the 'core correction' if there exists. | - | Also we can read the valence electrons number and the maximal | - | angular momentum used in this pseudopotential. We also read in the | - | trail wave function, trail atomic density and local-pseudopotential| - | on logrithmic grid. The non-local pseudopotential projector is also| - | read in if there is any. | - | | - <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - - - - PAO radial cut off (Bohr) = 15 - - Read in pseudopotential file is ./Si_ONCV_PBE-1.0.upf - pseudopotential type = NC - functional Ex = PBE - functional Ec = - functional GCEx = - functional GCEc = - nonlocal core correction = 0 - valence electrons = 4 - lmax = 1 - number of zeta = 0 - number of projectors = 4 - L of projector = 0 - L of projector = 0 - L of projector = 1 - L of projector = 1 - initial pseudo atomic orbital number = 0 - NLOCAL = 18 - - SETUP THE ELECTRONS NUMBER - electron number of element Si = 4 - total electron number of element Si = 8 - occupied bands = 4 - NBANDS = 8 - DONE : SETUP UNITCELL Time : 0.0648149461485 (SEC) - - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | Setup K-points | - | We setup the k-points according to input parameters. | - | The reduced k-points are set according to symmetry operations. | - | We treat the spin as another set of k-points. | - | | - <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - - - - - SETUP K-POINTS - nspin = 1 - Input type of k points = Monkhorst-Pack(Gamma) - nkstot = 8 - - KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT - 1 0 0 0 0.125 - 2 0.5 0 0 0.125 - 3 0 0.5 0 0.125 - 4 0.5 0.5 0 0.125 - 5 0 0 0.5 0.125 - 6 0.5 0 0.5 0.125 - 7 0 0.5 0.5 0.125 - 8 0.5 0.5 0.5 0.125 - - k-point number in this process = 8 - minimum distributed K point number = 8 - - KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT - 1 0 0 0 0.25 - 2 0.5 0.5 -0.5 0.25 - 3 0.5 -0.5 0.5 0.25 - 4 1 0 0 0.25 - 5 -0.5 0.5 0.5 0.25 - 6 0 1 0 0.25 - 7 0 0 1 0.25 - 8 0.5 0.5 0.5 0.25 - - KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT - 1 0 0 0 0.25 - 2 0.5 0 0 0.25 - 3 0 0.5 0 0.25 - 4 0.5 0.5 0 0.25 - 5 0 0 0.5 0.25 - 6 0.5 0 0.5 0.25 - 7 0 0.5 0.5 0.25 - 8 0.5 0.5 0.5 0.25 - DONE : INIT K-POINTS Time : 0.0652149026282 (SEC) - - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | Setup plane waves: | - | Use the energy cutoff and the lattice vectors to generate the | - | dimensions of FFT grid. The number of FFT grid on each processor | - | is 'nrxx'. The number of plane wave basis in reciprocal space is | - | different for charege/potential and wave functions. We also set | - | the 'sticks' for the parallel of FFT. | - | | - <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - - - - - SETUP THE PLANE WAVE BASIS - energy cutoff for wavefunc (unit:Ry) = 20 - [fft grid for wave functions] = 24, 24, 24 - [fft grid for charge/potential] = 24, 24, 24 - [fft grid division] = 1, 1, 1 - [big fft grid for charge/potential] = 24, 24, 24 - nbxx = 13824 - nrxx = 13824 - - SETUP PLANE WAVES FOR CHARGE/POTENTIAL - number of plane waves = 3143 - number of sticks = 283 - - SETUP PLANE WAVES FOR WAVE FUNCTIONS - number of plane waves = 609 - number of sticks = 91 - - PARALLEL PW FOR CHARGE/POTENTIAL - PROC COLUMNS(POT) PW - 1 283 3143 - --------------- sum ------------------- - 1 283 3143 - - PARALLEL PW FOR WAVE FUNCTIONS - PROC COLUMNS(W) PW - 1 91 609 - --------------- sum ------------------- - 1 91 609 - - SETUP COORDINATES OF PLANE WAVES - number of total plane waves = 3143 - - SETUP COORDINATES OF PLANE WAVES - number of |g| = 72 - max |g| = 208 - min |g| = 0 - DONE : INIT PLANEWAVE Time : 0.0986429497134 (SEC) - - npwx = 411 - - SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS - Si non-local projectors: - projector 1 L=0 - projector 2 L=0 - projector 3 L=1 - projector 4 L=1 - TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 - DONE : LOCAL POTENTIAL Time : 0.109992648242 (SEC) - - - Init Non-Local PseudoPotential table : - Init Non-Local-Pseudopotential done. - DONE : NON-LOCAL POTENTIAL Time : 0.122797146207 (SEC) - - start_pot = atomic - DONE : INIT POTENTIAL Time : 0.135785 (SEC) - - - Make real space PAO into reciprocal space. - max mesh points in Pseudopotential = 601 - dq(describe PAO in reciprocal space) = 0.01 - max q = 542 - - number of pseudo atomic orbitals for Si is 0 - DONE : INIT BASIS Time : 0.184089 (SEC) - - ...............Nose-Hoover Chain parameter initialization............... - Temperature = 3.16682e-05 - Temperature2 = 10.0004 - NHC frequency = 0.00120944 - NHC chain = 4 - Qmass = 1823.61 - ............................................................... - - PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- - K-point CG iter num Time(Sec) - 1 6.125000 0.314119 - 2 6.500000 0.327905 - 3 6.750000 0.334448 - 4 6.125000 0.309547 - 5 6.750000 0.112520 - 6 6.125000 0.024925 - 7 5.875000 0.024036 - 8 6.250000 0.025291 - - Density error is 0.108050841230 - - PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- - K-point CG iter num Time(Sec) - 1 2.500000 0.012342 - 2 2.250000 0.011339 - 3 2.625000 0.012621 - 4 3.250000 0.014770 - 5 2.500000 0.012183 - 6 3.125000 0.014333 - 7 2.125000 0.010831 - 8 2.625000 0.012575 - - Density error is 0.004334778560 - - PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- - K-point CG iter num Time(Sec) - 1 3.375000 0.015399 - 2 3.250000 0.014874 - 3 3.125000 0.014380 - 4 4.000000 0.017413 - 5 3.250000 0.014776 - 6 4.000000 0.017425 - 7 3.750000 0.016523 - 8 2.875000 0.013438 - - Density error is 0.000134739187 - - PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- - K-point CG iter num Time(Sec) - 1 3.750000 0.016717 - 2 3.250000 0.014854 - 3 3.375000 0.015229 - 4 4.000000 0.017399 - 5 3.500000 0.015669 - 6 4.000000 0.017380 - 7 4.500000 0.019148 - 8 3.375000 0.015188 - - Density error is 0.000014649703 - - PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- - K-point CG iter num Time(Sec) - 1 2.750000 0.013183 - 2 2.625000 0.012728 - 3 2.750000 0.013067 - 4 2.750000 0.013018 - 5 2.875000 0.013453 - 6 2.750000 0.013008 - 7 2.625000 0.012593 - 8 2.625000 0.012567 - - Density error is 0.000000599415 - - PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- - K-point CG iter num Time(Sec) - 1 3.125000 0.014489 - 2 3.625000 0.016131 - 3 3.250000 0.014781 - 4 4.375000 0.018739 - 5 3.375000 0.015250 - 6 4.000000 0.017425 - 7 4.250000 0.018253 - 8 3.375000 0.015213 - - Density error is 0.000000048534 - - PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- - K-point CG iter num Time(Sec) - 1 3.250000 0.015027 - 2 3.000000 0.013998 - 3 3.125000 0.014375 - 4 3.625000 0.016117 - 5 3.000000 0.013941 - 6 4.125000 0.017842 - 7 3.500000 0.015638 - 8 3.125000 0.014323 - - Density error is 0.000000002823 - - PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- - K-point CG iter num Time(Sec) - 1 3.500000 0.015909 - 2 3.125000 0.014437 - 3 3.000000 0.013954 - 4 3.500000 0.015692 - 5 3.250000 0.014873 - 6 3.250000 0.014791 - 7 3.375000 0.015237 - 8 3.125000 0.014335 - - Density error is 0.000000000061 - - charge density convergence is achieved - final etot is -211.771832657158 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.885363 +0.500467 +0.150240 - Si2 +0.885363 -0.500467 -0.150240 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.045273 -3.807537 -13.541448 - -3.807537 +124.421298 +24.047975 - -13.541448 +24.047975 +125.016023 - -output Pressure for check! -Virtual Pressure is +124.231102 Kbar -Virial is +124.160865 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 1 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564005 (Rydberg) - NVT Temperature : +10.000364 (K) - NVT Kinetic energy : +0.000190 (Rydberg) - NVT Potential energy : -15.564937 (Rydberg) - maxForce : +0.000400 - maxStep : +0.012800 - MD_STEP SystemE Conserved DeltaE Temperature - +1 -7.782469 -7.782003 +0.000000 +14.311776 - - PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +34.500000 +1.482434 - +2 +24.125000 +0.314735 - +3 +24.250000 +0.087904 - +4 +27.625000 +0.099392 - +5 +25.000000 +0.090634 - +6 +29.875000 +0.107431 - +7 +31.875000 +0.113921 - +8 +26.750000 +0.096067 - - Density error is +0.000008438536 - - PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010623 - +2 +2.000000 +0.010501 - +3 +2.000000 +0.010437 - +4 +2.000000 +0.010430 - +5 +2.000000 +0.010417 - +6 +2.000000 +0.010392 - +7 +2.000000 +0.010413 - +8 +2.000000 +0.010431 - - Density error is +0.000000589537 - - PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.375000 +0.011909 - +2 +2.125000 +0.010960 - +3 +2.125000 +0.010853 - +4 +2.750000 +0.013046 - +5 +2.000000 +0.010421 - +6 +2.750000 +0.013030 - +7 +3.375000 +0.015237 - +8 +2.125000 +0.010850 - - Density error is +0.000000029687 - - PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.375000 +0.015446 - +2 +3.500000 +0.015794 - +3 +3.125000 +0.014440 - +4 +3.500000 +0.015678 - +5 +3.625000 +0.016125 - +6 +3.500000 +0.015643 - +7 +3.250000 +0.014765 - +8 +3.500000 +0.015638 - - Density error is +0.000000000296 - - charge density convergence is achieved - final etot is -211.778481425683 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.815731 +0.355757 +0.109618 - Si2 +0.815731 -0.355757 -0.109618 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.843178 -2.800524 -9.609977 - -2.800524 +124.232437 +22.152784 - -9.609977 +22.152784 +124.529670 - -output Pressure for check! -Virtual Pressure is +123.968947 Kbar -Virial is +123.868428 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 2 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564050 (Rydberg) - NVT Temperature : +33.255982 (K) - NVT Kinetic energy : +0.000632 (Rydberg) - NVT Potential energy : -15.565426 (Rydberg) - maxForce : +0.000304 - maxStep : +0.026509 - MD_STEP SystemE Conserved DeltaE Temperature - +2 -7.782713 -7.782025 +0.000000 +66.542608 - - PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +33.625000 +1.455297 - +2 +23.000000 +0.344287 - +3 +23.250000 +0.084591 - +4 +27.250000 +0.097961 - +5 +24.625000 +0.089419 - +6 +28.375000 +0.101985 - +7 +26.625000 +0.096635 - +8 +24.625000 +0.089249 - - Density error is +0.000021869323 - - PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010696 - +2 +2.000000 +0.010427 - +3 +2.000000 +0.010429 - +4 +2.000000 +0.010408 - +5 +2.000000 +0.010427 - +6 +2.375000 +0.011750 - +7 +2.000000 +0.010404 - +8 +2.000000 +0.010397 - - Density error is +0.000001763699 - - PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011012 - +2 +2.250000 +0.011394 - +3 +2.250000 +0.011290 - +4 +2.875000 +0.013481 - +5 +2.250000 +0.011358 - +6 +3.000000 +0.013927 - +7 +2.875000 +0.013486 - +8 +2.375000 +0.011717 - - Density error is +0.000000036065 - - PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016348 - +2 +3.750000 +0.016579 - +3 +3.750000 +0.016547 - +4 +4.375000 +0.018704 - +5 +3.500000 +0.015695 - +6 +4.125000 +0.017849 - +7 +4.625000 +0.019620 - +8 +3.625000 +0.016087 - - Density error is +0.000000002244 - - PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013691 - +2 +3.000000 +0.013966 - +3 +2.875000 +0.013492 - +4 +3.875000 +0.016984 - +5 +3.250000 +0.014831 - +6 +3.750000 +0.016559 - +7 +3.000000 +0.013909 - +8 +3.000000 +0.013880 - - Density error is +0.000000000184 - - charge density convergence is achieved - final etot is -211.794269556733 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.462515 +0.083202 +0.018773 - Si2 +0.462515 -0.083202 -0.018773 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.815311 -0.492388 -2.246119 - -0.492388 +123.347654 +12.547878 - -2.246119 +12.547878 +123.364301 - -output Pressure for check! -Virtual Pressure is +123.643118 Kbar -Virial is +123.175755 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 3 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564151 (Rydberg) - NVT Temperature : +88.343003 (K) - NVT Kinetic energy : +0.001679 (Rydberg) - NVT Potential energy : -15.566586 (Rydberg) - maxForce : +0.000084 - maxStep : +0.033756 - MD_STEP SystemE Conserved DeltaE Temperature - +3 -7.783293 -7.782076 +0.000000 +112.977290 - - PW ALGORITHM --------------- ION=+4 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +37.125000 +1.584397 - +2 +24.625000 +0.212187 - +3 +25.750000 +0.092986 - +4 +29.250000 +0.104765 - +5 +27.000000 +0.097458 - +6 +31.875000 +0.113833 - +7 +28.250000 +0.101426 - +8 +25.250000 +0.091166 - - Density error is +0.000033429323 - - PW ALGORITHM --------------- ION=+4 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010606 - +2 +2.000000 +0.010470 - +3 +2.000000 +0.010394 - +4 +2.000000 +0.010391 - +5 +2.000000 +0.010403 - +6 +2.000000 +0.010374 - +7 +2.000000 +0.010374 - +8 +2.000000 +0.010432 - - Density error is +0.000002801781 - - PW ALGORITHM --------------- ION=+4 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011027 - +2 +2.500000 +0.012197 - +3 +2.250000 +0.011338 - +4 +2.375000 +0.011707 - +5 +2.250000 +0.011301 - +6 +2.625000 +0.012578 - +7 +2.875000 +0.013474 - +8 +2.375000 +0.011758 - - Density error is +0.000000035628 - - PW ALGORITHM --------------- ION=+4 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.875000 +0.017185 - +2 +3.875000 +0.017012 - +3 +3.750000 +0.016533 - +4 +4.000000 +0.017359 - +5 +3.750000 +0.016991 - +6 +3.875000 +0.017340 - +7 +4.625000 +0.019603 - +8 +3.750000 +0.016469 - - Density error is +0.000000003655 - - PW ALGORITHM --------------- ION=+4 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013239 - +2 +2.625000 +0.012645 - +3 +2.750000 +0.013035 - +4 +3.750000 +0.016496 - +5 +2.750000 +0.013016 - +6 +3.250000 +0.014762 - +7 +3.000000 +0.013915 - +8 +2.625000 +0.012541 - - Density error is +0.000000000196 - - charge density convergence is achieved - final etot is -211.798998994521 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.045801 -0.211053 -0.052135 - Si2 -0.045801 +0.211053 +0.052135 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.007250 +1.421851 +5.725860 - +1.421851 +122.897686 -1.245212 - +5.725860 -1.245212 +123.005310 - -output Pressure for check! -Virtual Pressure is +123.763579 Kbar -Virial is +122.970082 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 4 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564177 (Rydberg) - NVT Temperature : +103.974513 (K) - NVT Kinetic energy : +0.001976 (Rydberg) - NVT Potential energy : -15.566934 (Rydberg) - maxForce : +0.000019 - maxStep : +0.030839 - MD_STEP SystemE Conserved DeltaE Temperature - +4 -7.783467 -7.782089 +0.000000 +94.653093 - - PW ALGORITHM --------------- ION=+5 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.125000 +1.541803 - +2 +24.500000 +0.265063 - +3 +26.125000 +0.094359 - +4 +30.250000 +0.108286 - +5 +25.500000 +0.091682 - +6 +28.875000 +0.104719 - +7 +29.250000 +0.105021 - +8 +25.125000 +0.090821 - - Density error is +0.000028572302 - - PW ALGORITHM --------------- ION=+5 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010595 - +2 +2.000000 +0.010418 - +3 +2.000000 +0.010451 - +4 +2.000000 +0.010412 - +5 +2.000000 +0.010426 - +6 +2.000000 +0.010384 - +7 +2.000000 +0.010373 - +8 +2.000000 +0.010418 - - Density error is +0.000002384066 - - PW ALGORITHM --------------- ION=+5 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011011 - +2 +2.375000 +0.011743 - +3 +2.250000 +0.011317 - +4 +2.625000 +0.012578 - +5 +2.250000 +0.011279 - +6 +2.750000 +0.013007 - +7 +2.875000 +0.013443 - +8 +2.375000 +0.011684 - - Density error is +0.000000035575 - - PW ALGORITHM --------------- ION=+5 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016778 - +2 +3.875000 +0.017042 - +3 +3.750000 +0.016539 - +4 +4.125000 +0.017849 - +5 +3.750000 +0.016577 - +6 +3.625000 +0.016055 - +7 +4.625000 +0.019602 - +8 +3.625000 +0.016048 - - Density error is +0.000000003086 - - PW ALGORITHM --------------- ION=+5 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013198 - +2 +2.625000 +0.012687 - +3 +2.875000 +0.013502 - +4 +3.750000 +0.016536 - +5 +2.750000 +0.013120 - +6 +3.375000 +0.015253 - +7 +2.875000 +0.013430 - +8 +2.875000 +0.013424 - - Density error is +0.000000000189 - - charge density convergence is achieved - final etot is -211.787163106063 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.531795 -0.423861 -0.074943 - Si2 -0.531795 +0.423861 +0.074943 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.156562 +2.191352 +11.539648 - +2.191352 +123.421604 -14.461358 - +11.539648 -14.461358 +123.871961 - -output Pressure for check! -Virtual Pressure is +124.148173 Kbar -Virial is +123.483375 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 5 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564100 (Rydberg) - NVT Temperature : +61.015343 (K) - NVT Kinetic energy : +0.001159 (Rydberg) - NVT Potential energy : -15.566064 (Rydberg) - maxForce : +0.000177 - maxStep : +0.019294 - MD_STEP SystemE Conserved DeltaE Temperature - +5 -7.783032 -7.782050 +0.000000 +35.600513 - - PW ALGORITHM --------------- ION=+6 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.750000 +1.538779 - +2 +23.375000 +0.281560 - +3 +26.625000 +0.096030 - +4 +29.375000 +0.105067 - +5 +25.125000 +0.090691 - +6 +30.000000 +0.107285 - +7 +30.125000 +0.107224 - +8 +23.875000 +0.086308 - - Density error is +0.000013559050 - - PW ALGORITHM --------------- ION=+6 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010587 - +2 +2.000000 +0.010411 - +3 +2.000000 +0.010387 - +4 +2.000000 +0.010385 - +5 +2.000000 +0.010401 - +6 +2.000000 +0.010372 - +7 +2.000000 +0.010373 - +8 +2.000000 +0.010387 - - Density error is +0.000001049378 - - PW ALGORITHM --------------- ION=+6 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.010993 - +2 +2.125000 +0.010884 - +3 +2.125000 +0.010912 - +4 +2.500000 +0.012157 - +5 +2.125000 +0.010852 - +6 +2.750000 +0.013010 - +7 +3.000000 +0.013908 - +8 +2.125000 +0.010824 - - Density error is +0.000000034124 - - PW ALGORITHM --------------- ION=+6 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016280 - +2 +3.625000 +0.016107 - +3 +3.625000 +0.016126 - +4 +3.875000 +0.016930 - +5 +3.625000 +0.016102 - +6 +3.625000 +0.016047 - +7 +4.375000 +0.018675 - +8 +3.625000 +0.016036 - - Density error is +0.000000001047 - - PW ALGORITHM --------------- ION=+6 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.250000 +0.015029 - +2 +3.250000 +0.014818 - +3 +3.125000 +0.014333 - +4 +4.500000 +0.019099 - +5 +3.125000 +0.014369 - +6 +4.250000 +0.018282 - +7 +3.250000 +0.014734 - +8 +3.250000 +0.014725 - - Density error is +0.000000000093 - - charge density convergence is achieved - final etot is -211.773976096239 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.830073 -0.488698 -0.076368 - Si2 -0.830073 +0.488698 +0.076368 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.079115 +2.349387 +13.341463 - +2.349387 +124.240376 -22.607891 - +13.341463 -22.607891 +124.847553 - -output Pressure for check! -Virtual Pressure is +124.305722 Kbar -Virial is +124.055681 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 6 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564017 (Rydberg) - NVT Temperature : +13.869106 (K) - NVT Kinetic energy : +0.000264 (Rydberg) - NVT Potential energy : -15.565095 (Rydberg) - maxForce : +0.000353 - maxStep : +0.009591 - MD_STEP SystemE Conserved DeltaE Temperature - +6 -7.782547 -7.782009 +0.000000 +9.461554 - - PW ALGORITHM --------------- ION=+7 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.250000 +1.548029 - +2 +24.625000 +0.276619 - +3 +27.375000 +0.098665 - +4 +30.375000 +0.108527 - +5 +26.375000 +0.095093 - +6 +30.625000 +0.109686 - +7 +31.000000 +0.110332 - +8 +25.250000 +0.091074 - - Density error is +0.000006867857 - - PW ALGORITHM --------------- ION=+7 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010576 - +2 +2.000000 +0.010440 - +3 +2.000000 +0.010510 - +4 +2.000000 +0.010413 - +5 +2.000000 +0.010403 - +6 +2.125000 +0.010838 - +7 +2.000000 +0.010376 - +8 +2.000000 +0.010387 - - Density error is +0.000000471169 - - PW ALGORITHM --------------- ION=+7 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013211 - +2 +2.000000 +0.010520 - +3 +2.000000 +0.010489 - +4 +2.750000 +0.013013 - +5 +2.125000 +0.010843 - +6 +2.500000 +0.012183 - +7 +3.250000 +0.014821 - +8 +2.000000 +0.010417 - - Density error is +0.000000026949 - - PW ALGORITHM --------------- ION=+7 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.000000 +0.014095 - +2 +3.250000 +0.014863 - +3 +3.000000 +0.013942 - +4 +3.125000 +0.014354 - +5 +3.250000 +0.014813 - +6 +3.250000 +0.014752 - +7 +3.500000 +0.015640 - +8 +3.250000 +0.014764 - - Density error is +0.000000000178 - - charge density convergence is achieved - final etot is -211.775966500996 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.841211 -0.388251 -0.083865 - Si2 -0.841211 +0.388251 +0.083865 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.888185 +2.498229 +10.607911 - +2.498229 +124.324706 -22.903208 - +10.607911 -22.903208 +124.699212 - -output Pressure for check! -Virtual Pressure is +124.037154 Kbar -Virial is +123.970701 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 7 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564029 (Rydberg) - NVT Temperature : +20.830773 (K) - NVT Kinetic energy : +0.000396 (Rydberg) - NVT Potential energy : -15.565241 (Rydberg) - maxForce : +0.000327 - maxStep : +0.022260 - MD_STEP SystemE Conserved DeltaE Temperature - +7 -7.782620 -7.782015 +0.000000 +47.763680 - - PW ALGORITHM --------------- ION=+8 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +34.625000 +1.498024 - +2 +22.500000 +0.296778 - +3 +24.500000 +0.088638 - +4 +28.750000 +0.103008 - +5 +24.000000 +0.086877 - +6 +29.375000 +0.105138 - +7 +26.250000 +0.094433 - +8 +22.375000 +0.081172 - - Density error is +0.000016498376 - - PW ALGORITHM --------------- ION=+8 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010574 - +2 +2.000000 +0.010443 - +3 +2.000000 +0.010379 - +4 +2.000000 +0.010399 - +5 +2.000000 +0.010420 - +6 +2.000000 +0.010425 - +7 +2.500000 +0.012164 - +8 +2.000000 +0.010416 - - Density error is +0.000001314992 - - PW ALGORITHM --------------- ION=+8 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011051 - +2 +2.250000 +0.011345 - +3 +2.125000 +0.010869 - +4 +2.750000 +0.013016 - +5 +2.250000 +0.011286 - +6 +2.750000 +0.013011 - +7 +3.125000 +0.014347 - +8 +2.250000 +0.011259 - - Density error is +0.000000033932 - - PW ALGORITHM --------------- ION=+8 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.017140 - +2 +3.625000 +0.016310 - +3 +3.750000 +0.016631 - +4 +4.000000 +0.017495 - +5 +3.500000 +0.015705 - +6 +4.125000 +0.017878 - +7 +4.250000 +0.018300 - +8 +3.500000 +0.015635 - - Density error is +0.000000001483 - - PW ALGORITHM --------------- ION=+8 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013210 - +2 +3.125000 +0.014428 - +3 +3.125000 +0.014340 - +4 +4.000000 +0.017385 - +5 +3.125000 +0.014518 - +6 +3.625000 +0.016115 - +7 +3.500000 +0.015627 - +8 +3.375000 +0.015173 - - Density error is +0.000000000115 - - charge density convergence is achieved - final etot is -211.790638622284 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.562521 -0.158433 -0.082597 - Si2 -0.562521 +0.158433 +0.082597 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.818911 +2.300863 +4.331819 - +2.300863 +123.569280 -15.284717 - +4.331819 -15.284717 +123.616732 - -output Pressure for check! -Virtual Pressure is +123.670443 Kbar -Virial is +123.334974 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 8 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564121 (Rydberg) - NVT Temperature : +72.197413 (K) - NVT Kinetic energy : +0.001372 (Rydberg) - NVT Potential energy : -15.566319 (Rydberg) - maxForce : +0.000132 - maxStep : +0.031989 - MD_STEP SystemE Conserved DeltaE Temperature - +8 -7.783160 -7.782060 +0.000000 +101.706395 - - PW ALGORITHM --------------- ION=+9 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.875000 +1.531937 - +2 +26.875000 +0.264962 - +3 +26.750000 +0.096733 - +4 +30.375000 +0.108739 - +5 +27.000000 +0.097620 - +6 +31.875000 +0.114026 - +7 +28.000000 +0.100499 - +8 +25.250000 +0.092090 - - Density error is +0.000030268617 - - PW ALGORITHM --------------- ION=+9 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010942 - +2 +2.000000 +0.010442 - +3 +2.000000 +0.010413 - +4 +2.000000 +0.010444 - +5 +2.000000 +0.010413 - +6 +2.000000 +0.010372 - +7 +2.000000 +0.010379 - +8 +2.000000 +0.010382 - - Density error is +0.000002526424 - - PW ALGORITHM --------------- ION=+9 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011021 - +2 +2.500000 +0.012194 - +3 +2.250000 +0.011346 - +4 +2.375000 +0.011731 - +5 +2.250000 +0.011785 - +6 +2.750000 +0.013400 - +7 +2.875000 +0.013483 - +8 +2.500000 +0.012132 - - Density error is +0.000000035287 - - PW ALGORITHM --------------- ION=+9 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016272 - +2 +3.750000 +0.016595 - +3 +3.625000 +0.016152 - +4 +3.875000 +0.016950 - +5 +3.625000 +0.016113 - +6 +3.750000 +0.016497 - +7 +4.625000 +0.019580 - +8 +3.750000 +0.016488 - - Density error is +0.000000003280 - - PW ALGORITHM --------------- ION=+9 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013195 - +2 +2.750000 +0.013069 - +3 +2.875000 +0.013452 - +4 +4.250000 +0.018388 - +5 +2.875000 +0.013480 - +6 +3.500000 +0.015655 - +7 +3.000000 +0.013869 - +8 +2.625000 +0.012553 - - Density error is +0.000000000193 - - charge density convergence is achieved - final etot is -211.799689533651 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.088600 +0.125590 -0.036123 - Si2 -0.088600 -0.125590 +0.036123 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.942319 +0.972401 -3.404364 - +0.972401 +122.922036 -2.403271 - -3.404364 -2.403271 +122.959321 - -output Pressure for check! -Virtual Pressure is +123.655562 Kbar -Virial is +122.941225 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 9 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564178 (Rydberg) - NVT Temperature : +102.774866 (K) - NVT Kinetic energy : +0.001953 (Rydberg) - NVT Potential energy : -15.566984 (Rydberg) - maxForce : +0.000009 - maxStep : +0.032288 - MD_STEP SystemE Conserved DeltaE Temperature - +9 -7.783492 -7.782089 +0.000000 +102.692994 - - PW ALGORITHM --------------- ION=+10 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.000000 +1.538429 - +2 +24.875000 +0.260502 - +3 +25.750000 +0.093167 - +4 +29.875000 +0.106972 - +5 +26.000000 +0.094130 - +6 +30.000000 +0.107537 - +7 +31.000000 +0.110836 - +8 +25.375000 +0.091698 - - Density error is +0.000030737201 - - PW ALGORITHM --------------- ION=+10 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010666 - +2 +2.000000 +0.010444 - +3 +2.000000 +0.010477 - +4 +2.000000 +0.010404 - +5 +2.000000 +0.010414 - +6 +2.000000 +0.010377 - +7 +2.000000 +0.010374 - +8 +2.000000 +0.010388 - - Density error is +0.000002560646 - - PW ALGORITHM --------------- ION=+10 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.250000 +0.011451 - +2 +2.500000 +0.012257 - +3 +2.250000 +0.011301 - +4 +2.750000 +0.013040 - +5 +2.250000 +0.011288 - +6 +2.625000 +0.012593 - +7 +3.000000 +0.013923 - +8 +2.500000 +0.012151 - - Density error is +0.000000033975 - - PW ALGORITHM --------------- ION=+10 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016339 - +2 +3.875000 +0.017015 - +3 +3.750000 +0.016527 - +4 +4.250000 +0.018269 - +5 +3.750000 +0.016535 - +6 +3.750000 +0.016493 - +7 +4.625000 +0.019590 - +8 +3.750000 +0.016482 - - Density error is +0.000000003387 - - PW ALGORITHM --------------- ION=+10 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013682 - +2 +2.625000 +0.012626 - +3 +2.750000 +0.013042 - +4 +3.750000 +0.016591 - +5 +3.000000 +0.013926 - +6 +3.500000 +0.015660 - +7 +3.000000 +0.013942 - +8 +2.625000 +0.012582 - - Density error is +0.000000000211 - - charge density convergence is achieved - final etot is -211.791757080168 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.416931 +0.372190 +0.054656 - Si2 +0.416931 -0.372190 -0.054656 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.112004 -1.386177 -10.090684 - -1.386177 +123.202765 +11.305489 - -10.090684 +11.305489 +123.552704 - -output Pressure for check! -Virtual Pressure is +124.010423 Kbar -Virial is +123.289157 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 10 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564126 (Rydberg) - NVT Temperature : +73.190993 (K) - NVT Kinetic energy : +0.001391 (Rydberg) - NVT Potential energy : -15.566401 (Rydberg) - maxForce : +0.000119 - maxStep : +0.022835 - MD_STEP SystemE Conserved DeltaE Temperature - +10 -7.783201 -7.782063 +0.000000 +48.734190 - - PW ALGORITHM --------------- ION=+11 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.875000 +1.541778 - +2 +25.500000 +0.266144 - +3 +25.250000 +0.091185 - +4 +29.250000 +0.104785 - +5 +24.875000 +0.090153 - +6 +30.625000 +0.109517 - +7 +28.875000 +0.103393 - +8 +27.500000 +0.098937 - - Density error is +0.000016935127 - - PW ALGORITHM --------------- ION=+11 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010679 - +2 +2.000000 +0.010521 - +3 +2.000000 +0.010402 - +4 +2.000000 +0.010379 - +5 +2.000000 +0.010446 - +6 +2.000000 +0.010416 - +7 +2.000000 +0.010382 - +8 +2.000000 +0.010370 - - Density error is +0.000001343508 - - PW ALGORITHM --------------- ION=+11 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.010997 - +2 +2.125000 +0.010874 - +3 +2.250000 +0.011252 - +4 +2.625000 +0.012581 - +5 +2.125000 +0.010886 - +6 +2.625000 +0.012585 - +7 +3.000000 +0.013888 - +8 +2.375000 +0.011709 - - Density error is +0.000000032255 - - PW ALGORITHM --------------- ION=+11 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016894 - +2 +3.750000 +0.016617 - +3 +3.625000 +0.016129 - +4 +3.875000 +0.016962 - +5 +3.750000 +0.016549 - +6 +3.750000 +0.016487 - +7 +4.500000 +0.019118 - +8 +3.500000 +0.015592 - - Density error is +0.000000001579 - - PW ALGORITHM --------------- ION=+11 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013663 - +2 +3.125000 +0.014367 - +3 +2.875000 +0.013494 - +4 +4.125000 +0.017819 - +5 +3.125000 +0.014308 - +6 +4.000000 +0.017389 - +7 +3.125000 +0.014286 - +8 +3.125000 +0.014297 - - Density error is +0.000000000113 - - charge density convergence is achieved - final etot is -211.777136772291 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.774114 +0.493555 +0.132287 - Si2 +0.774114 -0.493555 -0.132287 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.125513 -3.354234 -13.360634 - -3.354234 +124.042603 +21.012997 - -13.360634 +21.012997 +124.630461 - -output Pressure for check! -Virtual Pressure is +124.275144 Kbar -Virial is +123.932859 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 11 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564029 (Rydberg) - NVT Temperature : +20.916618 (K) - NVT Kinetic energy : +0.000397 (Rydberg) - NVT Potential energy : -15.565327 (Rydberg) - maxForce : +0.000325 - maxStep : +0.009427 - MD_STEP SystemE Conserved DeltaE Temperature - +11 -7.782663 -7.782015 +0.000000 +9.036895 - - PW ALGORITHM --------------- ION=+12 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.125000 +1.547415 - +2 +26.375000 +0.264168 - +3 +25.375000 +0.091673 - +4 +29.500000 +0.105644 - +5 +26.125000 +0.094314 - +6 +31.500000 +0.112479 - +7 +29.875000 +0.106803 - +8 +28.625000 +0.102367 - - Density error is +0.000006530970 - - PW ALGORITHM --------------- ION=+12 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010577 - +2 +2.000000 +0.010466 - +3 +2.000000 +0.010402 - +4 +2.000000 +0.010371 - +5 +2.000000 +0.010404 - +6 +2.000000 +0.010385 - +7 +2.000000 +0.010377 - +8 +2.000000 +0.010356 - - Density error is +0.000000440898 - - PW ALGORITHM --------------- ION=+12 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.625000 +0.012786 - +2 +2.000000 +0.010477 - +3 +2.000000 +0.010393 - +4 +2.750000 +0.013027 - +5 +2.125000 +0.010923 - +6 +2.750000 +0.012995 - +7 +3.125000 +0.014337 - +8 +2.000000 +0.010365 - - Density error is +0.000000024207 - - PW ALGORITHM --------------- ION=+12 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.000000 +0.014107 - +2 +3.125000 +0.014392 - +3 +3.000000 +0.013912 - +4 +3.375000 +0.015251 - +5 +3.375000 +0.015234 - +6 +3.125000 +0.014438 - +7 +3.250000 +0.014784 - +8 +3.250000 +0.014731 - - Density error is +0.000000000170 - - charge density convergence is achieved - final etot is -211.774943325509 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.854779 +0.436696 +0.135045 - Si2 +0.854779 -0.436696 -0.135045 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.950297 -3.436598 -11.810037 - -3.436598 +124.343261 +23.217684 - -11.810037 +23.217684 +124.792605 - -output Pressure for check! -Virtual Pressure is +124.092191 Kbar -Virial is +124.028721 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 12 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564015 (Rydberg) - NVT Temperature : +13.061843 (K) - NVT Kinetic energy : +0.000248 (Rydberg) - NVT Potential energy : -15.565166 (Rydberg) - maxForce : +0.000355 - maxStep : +0.019395 - MD_STEP SystemE Conserved DeltaE Temperature - +12 -7.782583 -7.782007 +0.000000 +34.185920 - - PW ALGORITHM --------------- ION=+13 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +34.000000 +1.465002 - +2 +23.000000 +0.338683 - +3 +23.500000 +0.085138 - +4 +27.875000 +0.099984 - +5 +24.000000 +0.086926 - +6 +28.875000 +0.103425 - +7 +30.250000 +0.108009 - +8 +24.000000 +0.086816 - - Density error is +0.000013073792 - - PW ALGORITHM --------------- ION=+13 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010625 - +2 +2.000000 +0.010427 - +3 +2.000000 +0.010396 - +4 +2.000000 +0.010386 - +5 +2.000000 +0.010431 - +6 +2.000000 +0.010378 - +7 +2.000000 +0.010379 - +8 +2.000000 +0.010393 - - Density error is +0.000001008013 - - PW ALGORITHM --------------- ION=+13 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011016 - +2 +2.250000 +0.011351 - +3 +2.125000 +0.010831 - +4 +2.750000 +0.013017 - +5 +2.125000 +0.010830 - +6 +2.750000 +0.013067 - +7 +3.125000 +0.014333 - +8 +2.250000 +0.011270 - - Density error is +0.000000030793 - - PW ALGORITHM --------------- ION=+13 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016352 - +2 +3.500000 +0.015679 - +3 +3.625000 +0.016117 - +4 +3.875000 +0.016947 - +5 +3.625000 +0.016079 - +6 +3.750000 +0.016476 - +7 +4.250000 +0.018229 - +8 +3.500000 +0.015618 - - Density error is +0.000000001065 - - PW ALGORITHM --------------- ION=+13 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013652 - +2 +3.375000 +0.015279 - +3 +3.125000 +0.014327 - +4 +4.125000 +0.017830 - +5 +3.250000 +0.014748 - +6 +4.250000 +0.018231 - +7 +3.500000 +0.015621 - +8 +3.375000 +0.015172 - - Density error is +0.000000000097 - - charge density convergence is achieved - final etot is -211.787892336077 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.634765 +0.219902 +0.063772 - Si2 +0.634765 -0.219902 -0.063772 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.810989 -1.646977 -5.949715 - -1.646977 +123.724465 +17.235456 - -5.949715 +17.235456 +123.839274 - -output Pressure for check! -Virtual Pressure is +123.698348 Kbar -Virial is +123.458243 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 13 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564100 (Rydberg) - NVT Temperature : +58.268396 (K) - NVT Kinetic energy : +0.001107 (Rydberg) - NVT Potential energy : -15.566117 (Rydberg) - maxForce : +0.000172 - maxStep : +0.030214 - MD_STEP SystemE Conserved DeltaE Temperature - +13 -7.783059 -7.782050 +0.000000 +89.458675 - - PW ALGORITHM --------------- ION=+14 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.875000 +1.542133 - +2 +26.125000 +0.252769 - +3 +27.000000 +0.097434 - +4 +31.125000 +0.111257 - +5 +27.250000 +0.098368 - +6 +30.375000 +0.108770 - +7 +28.125000 +0.101032 - +8 +27.000000 +0.097412 - - Density error is +0.000027152014 - - PW ALGORITHM --------------- ION=+14 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010571 - +2 +2.000000 +0.010418 - +3 +2.000000 +0.010469 - +4 +2.000000 +0.010378 - +5 +2.000000 +0.010391 - +6 +2.125000 +0.010816 - +7 +2.000000 +0.010413 - +8 +2.000000 +0.010387 - - Density error is +0.000002253887 - - PW ALGORITHM --------------- ION=+14 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011042 - +2 +2.375000 +0.011756 - +3 +2.250000 +0.011280 - +4 +2.750000 +0.013020 - +5 +2.250000 +0.011259 - +6 +2.625000 +0.012556 - +7 +2.875000 +0.013452 - +8 +2.500000 +0.012282 - - Density error is +0.000000033052 - - PW ALGORITHM --------------- ION=+14 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.875000 +0.017209 - +2 +3.750000 +0.016568 - +3 +3.625000 +0.016133 - +4 +4.250000 +0.018248 - +5 +3.625000 +0.016119 - +6 +4.250000 +0.018240 - +7 +4.750000 +0.020036 - +8 +3.625000 +0.016022 - - Density error is +0.000000002963 - - PW ALGORITHM --------------- ION=+14 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013700 - +2 +2.750000 +0.013049 - +3 +2.750000 +0.012990 - +4 +3.500000 +0.015607 - +5 +3.000000 +0.013859 - +6 +3.375000 +0.015179 - +7 +2.875000 +0.013422 - +8 +2.750000 +0.012955 - - Density error is +0.000000000187 - - charge density convergence is achieved - final etot is -211.799136169946 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.198870 -0.070672 -0.020734 - Si2 +0.198870 +0.070672 +0.020734 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.902575 +0.551658 +1.913429 - +0.551658 +122.991496 +5.397063 - +1.913429 +5.397063 +123.003398 - -output Pressure for check! -Virtual Pressure is +123.594137 Kbar -Virial is +122.965823 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 14 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564168 (Rydberg) - NVT Temperature : +96.770497 (K) - NVT Kinetic energy : +0.001839 (Rydberg) - NVT Potential energy : -15.566944 (Rydberg) - maxForce : +0.000017 - maxStep : +0.032116 - MD_STEP SystemE Conserved DeltaE Temperature - +14 -7.783472 -7.782084 +0.000000 +103.109630 - - PW ALGORITHM --------------- ION=+15 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.375000 +1.505918 - +2 +24.375000 +0.254664 - +3 +24.625000 +0.089084 - +4 +30.625000 +0.109605 - +5 +26.625000 +0.095625 - +6 +29.125000 +0.104515 - +7 +27.875000 +0.100128 - +8 +24.500000 +0.088547 - - Density error is +0.000030393373 - - PW ALGORITHM --------------- ION=+15 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010563 - +2 +2.000000 +0.010432 - +3 +2.000000 +0.010404 - +4 +2.000000 +0.010375 - +5 +2.000000 +0.010381 - +6 +2.000000 +0.010377 - +7 +2.000000 +0.010377 - +8 +2.000000 +0.010354 - - Density error is +0.000002547296 - - PW ALGORITHM --------------- ION=+15 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.250000 +0.011476 - +2 +2.500000 +0.012193 - +3 +2.250000 +0.011277 - +4 +2.750000 +0.013015 - +5 +2.250000 +0.011319 - +6 +2.750000 +0.013017 - +7 +2.750000 +0.013009 - +8 +2.500000 +0.012125 - - Density error is +0.000000032257 - - PW ALGORITHM --------------- ION=+15 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016335 - +2 +3.875000 +0.016993 - +3 +3.750000 +0.016491 - +4 +4.375000 +0.018723 - +5 +3.750000 +0.016532 - +6 +3.500000 +0.015608 - +7 +4.375000 +0.018691 - +8 +3.750000 +0.016462 - - Density error is +0.000000003366 - - PW ALGORITHM --------------- ION=+15 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013287 - +2 +2.625000 +0.012630 - +3 +2.875000 +0.013438 - +4 +3.500000 +0.015728 - +5 +2.750000 +0.013063 - +6 +3.125000 +0.014314 - +7 +3.250000 +0.014752 - +8 +2.625000 +0.012547 - - Density error is +0.000000000185 - - charge density convergence is achieved - final etot is -211.794739884606 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.297987 -0.327806 -0.066082 - Si2 -0.297987 +0.327806 +0.066082 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.100328 +1.856002 +8.909136 - +1.856002 +123.052207 -8.099784 - +8.909136 -8.099784 +123.317967 - -output Pressure for check! -Virtual Pressure is +123.881026 Kbar -Virial is +123.156834 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 15 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564136 (Rydberg) - NVT Temperature : +79.642870 (K) - NVT Kinetic energy : +0.001513 (Rydberg) - NVT Potential energy : -15.566621 (Rydberg) - maxForce : +0.000076 - maxStep : +0.024468 - MD_STEP SystemE Conserved DeltaE Temperature - +15 -7.783310 -7.782068 +0.000000 +58.786721 - - PW ALGORITHM --------------- ION=+16 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.000000 +1.550421 - +2 +24.125000 +0.253604 - +3 +26.125000 +0.094431 - +4 +29.625000 +0.106054 - +5 +25.500000 +0.091700 - +6 +29.500000 +0.105684 - +7 +29.125000 +0.104354 - +8 +23.750000 +0.086118 - - Density error is +0.000019003017 - - PW ALGORITHM --------------- ION=+16 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010587 - +2 +2.000000 +0.010446 - +3 +2.000000 +0.010445 - +4 +2.000000 +0.010404 - +5 +2.000000 +0.010390 - +6 +2.000000 +0.010379 - +7 +2.000000 +0.010378 - +8 +2.000000 +0.010370 - - Density error is +0.000001546864 - - PW ALGORITHM --------------- ION=+16 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011046 - +2 +2.375000 +0.011756 - +3 +2.250000 +0.011289 - +4 +2.500000 +0.012140 - +5 +2.250000 +0.011313 - +6 +2.750000 +0.013017 - +7 +2.875000 +0.013462 - +8 +2.250000 +0.011249 - - Density error is +0.000000031769 - - PW ALGORITHM --------------- ION=+16 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016761 - +2 +3.500000 +0.015694 - +3 +3.750000 +0.016521 - +4 +4.000000 +0.017360 - +5 +3.500000 +0.015655 - +6 +3.625000 +0.016032 - +7 +4.625000 +0.019569 - +8 +3.625000 +0.016039 - - Density error is +0.000000001918 - - PW ALGORITHM --------------- ION=+16 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013196 - +2 +3.125000 +0.014455 - +3 +2.875000 +0.013481 - +4 +4.000000 +0.017394 - +5 +3.000000 +0.013924 - +6 +3.750000 +0.016493 - +7 +3.000000 +0.013924 - +8 +3.125000 +0.014310 - - Density error is +0.000000000142 - - charge density convergence is achieved - final etot is -211.780796729120 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.685454 -0.466777 -0.074732 - Si2 -0.685454 +0.466777 +0.074732 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.145046 +2.237882 +12.724721 - +2.237882 +123.794533 -18.656690 - +12.724721 -18.656690 +124.345426 - -output Pressure for check! -Virtual Pressure is +124.174558 Kbar -Virial is +123.761668 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 16 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564047 (Rydberg) - NVT Temperature : +29.284447 (K) - NVT Kinetic energy : +0.000556 (Rydberg) - NVT Potential energy : -15.565596 (Rydberg) - maxForce : +0.000262 - maxStep : +0.011494 - MD_STEP SystemE Conserved DeltaE Temperature - +16 -7.782798 -7.782023 +0.000000 +12.500370 - - PW ALGORITHM --------------- ION=+17 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.250000 +1.548769 - +2 +24.250000 +0.238733 - +3 +26.875000 +0.097094 - +4 +30.500000 +0.109091 - +5 +25.500000 +0.092283 - +6 +29.500000 +0.106987 - +7 +30.375000 +0.108359 - +8 +24.000000 +0.086977 - - Density error is +0.000007183223 - - PW ALGORITHM --------------- ION=+17 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010577 - +2 +2.000000 +0.010427 - +3 +2.000000 +0.010496 - +4 +2.000000 +0.010394 - +5 +2.000000 +0.010418 - +6 +2.125000 +0.010931 - +7 +2.000000 +0.010379 - +8 +2.000000 +0.010422 - - Density error is +0.000000511477 - - PW ALGORITHM --------------- ION=+17 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.375000 +0.011921 - +2 +2.125000 +0.010910 - +3 +2.125000 +0.010844 - +4 +2.875000 +0.013531 - +5 +2.000000 +0.010405 - +6 +2.625000 +0.012594 - +7 +3.375000 +0.015197 - +8 +2.125000 +0.010844 - - Density error is +0.000000026283 - - PW ALGORITHM --------------- ION=+17 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.375000 +0.015456 - +2 +3.625000 +0.016132 - +3 +3.250000 +0.014828 - +4 +3.500000 +0.015635 - +5 +3.375000 +0.015239 - +6 +3.375000 +0.015161 - +7 +3.125000 +0.014336 - +8 +3.500000 +0.015643 - - Density error is +0.000000000237 - - charge density convergence is achieved - final etot is -211.774985509926 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.833310 -0.445812 -0.078719 - Si2 -0.833310 +0.445812 +0.078719 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.994195 +2.379118 +12.171980 - +2.379118 +124.272817 -22.694125 - +12.171980 -22.694125 +124.774373 - -output Pressure for check! -Virtual Pressure is +124.101591 Kbar -Virial is +124.013795 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 17 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564010 (Rydberg) - NVT Temperature : +8.524394 (K) - NVT Kinetic energy : +0.000162 (Rydberg) - NVT Potential energy : -15.565169 (Rydberg) - maxForce : +0.000340 - maxStep : +0.014988 - MD_STEP SystemE Conserved DeltaE Temperature - +17 -7.782584 -7.782005 +0.000000 +21.039416 - - PW ALGORITHM --------------- ION=+18 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +34.250000 +1.473409 - +2 +22.000000 +0.326542 - +3 +24.000000 +0.087028 - +4 +28.000000 +0.100599 - +5 +24.000000 +0.086910 - +6 +29.000000 +0.103884 - +7 +27.125000 +0.097431 - +8 +21.625000 +0.078627 - - Density error is +0.000009301236 - - PW ALGORITHM --------------- ION=+18 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010625 - +2 +2.000000 +0.010448 - +3 +2.000000 +0.010394 - +4 +2.000000 +0.010369 - +5 +2.000000 +0.010395 - +6 +2.125000 +0.010809 - +7 +2.000000 +0.010374 - +8 +2.000000 +0.010352 - - Density error is +0.000000698839 - - PW ALGORITHM --------------- ION=+18 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.250000 +0.011468 - +2 +2.125000 +0.010873 - +3 +2.125000 +0.010841 - +4 +2.875000 +0.013464 - +5 +2.125000 +0.010821 - +6 +2.500000 +0.012141 - +7 +3.125000 +0.014320 - +8 +2.125000 +0.010803 - - Density error is +0.000000028756 - - PW ALGORITHM --------------- ION=+18 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.500000 +0.015856 - +2 +3.625000 +0.016113 - +3 +3.500000 +0.015631 - +4 +3.625000 +0.016042 - +5 +3.625000 +0.016071 - +6 +3.750000 +0.016468 - +7 +4.000000 +0.017389 - +8 +3.625000 +0.016045 - - Density error is +0.000000000545 - - charge density convergence is achieved - final etot is -211.784530531570 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.693682 -0.275109 -0.084557 - Si2 -0.693682 +0.275109 +0.084557 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.844932 +2.424056 +7.513685 - +2.424056 +123.890142 -18.864028 - +7.513685 -18.864028 +124.067900 - -output Pressure for check! -Virtual Pressure is +123.748762 Kbar -Virial is +123.600991 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 18 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564069 (Rydberg) - NVT Temperature : +42.047874 (K) - NVT Kinetic energy : +0.000799 (Rydberg) - NVT Potential energy : -15.565870 (Rydberg) - maxForce : +0.000213 - maxStep : +0.027051 - MD_STEP SystemE Conserved DeltaE Temperature - +18 -7.782935 -7.782034 +0.000000 +72.297418 - - PW ALGORITHM --------------- ION=+19 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +33.625000 +1.446761 - +2 +22.750000 +0.337746 - +3 +24.500000 +0.088664 - +4 +26.875000 +0.096374 - +5 +24.375000 +0.088118 - +6 +27.625000 +0.099005 - +7 +26.125000 +0.093894 - +8 +23.000000 +0.083275 - - Density error is +0.000022341414 - - PW ALGORITHM --------------- ION=+19 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010590 - +2 +2.000000 +0.010429 - +3 +2.000000 +0.010400 - +4 +2.500000 +0.012143 - +5 +2.000000 +0.010418 - +6 +2.000000 +0.010354 - +7 +2.375000 +0.011685 - +8 +2.000000 +0.010357 - - Density error is +0.000001840522 - - PW ALGORITHM --------------- ION=+19 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011068 - +2 +2.375000 +0.011775 - +3 +2.250000 +0.011276 - +4 +2.500000 +0.012134 - +5 +2.250000 +0.011291 - +6 +2.500000 +0.012133 - +7 +3.000000 +0.013910 - +8 +2.375000 +0.011695 - - Density error is +0.000000031328 - - PW ALGORITHM --------------- ION=+19 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016750 - +2 +3.750000 +0.016541 - +3 +3.750000 +0.016522 - +4 +4.000000 +0.017360 - +5 +3.625000 +0.016071 - +6 +3.875000 +0.016922 - +7 +4.125000 +0.017815 - +8 +3.875000 +0.016914 - - Density error is +0.000000002386 - - PW ALGORITHM --------------- ION=+19 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013224 - +2 +2.875000 +0.013511 - +3 +2.875000 +0.013467 - +4 +3.875000 +0.016967 - +5 +2.875000 +0.013449 - +6 +3.500000 +0.015602 - +7 +3.500000 +0.015614 - +8 +2.500000 +0.012112 - - Density error is +0.000000000165 - - charge density convergence is achieved - final etot is -211.797509996802 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.315435 -0.012610 -0.062567 - Si2 -0.315435 +0.012610 +0.062567 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.869560 +1.699030 +0.355976 - +1.699030 +123.125358 -8.562365 - +0.355976 -8.562365 +123.115733 - -output Pressure for check! -Virtual Pressure is +123.544666 Kbar -Virial is +123.036884 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 19 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564150 (Rydberg) - NVT Temperature : +86.724314 (K) - NVT Kinetic energy : +0.001648 (Rydberg) - NVT Potential energy : -15.566824 (Rydberg) - maxForce : +0.000039 - maxStep : +0.031849 - MD_STEP SystemE Conserved DeltaE Temperature - +19 -7.783412 -7.782075 +0.000000 +101.072847 - - PW ALGORITHM --------------- ION=+20 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.000000 +1.535621 - +2 +25.500000 +0.274161 - +3 +26.125000 +0.094184 - +4 +29.875000 +0.106798 - +5 +26.375000 +0.095103 - +6 +30.750000 +0.109985 - +7 +31.875000 +0.114172 - +8 +25.750000 +0.092841 - - Density error is +0.000029792721 - - PW ALGORITHM --------------- ION=+20 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011051 - +2 +2.000000 +0.010426 - +3 +2.000000 +0.010378 - +4 +2.125000 +0.010793 - +5 +2.000000 +0.010367 - +6 +2.000000 +0.010355 - +7 +2.000000 +0.010362 - +8 +2.000000 +0.010354 - - Density error is +0.000002500903 - - PW ALGORITHM --------------- ION=+20 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.375000 +0.011932 - +2 +2.500000 +0.012164 - +3 +2.250000 +0.011253 - +4 +2.500000 +0.012117 - +5 +2.250000 +0.011252 - +6 +2.750000 +0.012983 - +7 +2.750000 +0.013005 - +8 +2.500000 +0.012105 - - Density error is +0.000000031164 - - PW ALGORITHM --------------- ION=+20 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016752 - +2 +3.875000 +0.016963 - +3 +3.750000 +0.016481 - +4 +3.875000 +0.016934 - +5 +3.750000 +0.016474 - +6 +3.625000 +0.016019 - +7 +4.750000 +0.019994 - +8 +3.750000 +0.016447 - - Density error is +0.000000003269 - - PW ALGORITHM --------------- ION=+20 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013655 - +2 +2.625000 +0.012594 - +3 +2.625000 +0.012553 - +4 +3.750000 +0.016475 - +5 +2.875000 +0.013402 - +6 +3.500000 +0.015683 - +7 +2.750000 +0.012961 - +8 +2.625000 +0.012526 - - Density error is +0.000000000179 - - charge density convergence is achieved - final etot is -211.797737534802 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.171785 +0.257041 +0.008602 - Si2 +0.171785 -0.257041 -0.008602 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.033300 -0.204765 -6.972062 - -0.204765 +122.939153 +4.657249 - -6.972062 +4.657249 +123.108999 - -output Pressure for check! -Virtual Pressure is +123.737037 Kbar -Virial is +123.027151 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 20 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564150 (Rydberg) - NVT Temperature : +85.566203 (K) - NVT Kinetic energy : +0.001626 (Rydberg) - NVT Potential energy : -15.566841 (Rydberg) - maxForce : +0.000036 - maxStep : +0.026933 - MD_STEP SystemE Conserved DeltaE Temperature - +20 -7.783421 -7.782075 +0.000000 +70.314105 - - PW ALGORITHM --------------- ION=+21 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.125000 +1.533770 - +2 +24.250000 +0.243025 - +3 +24.750000 +0.089487 - +4 +29.750000 +0.106362 - +5 +24.875000 +0.089914 - +6 +29.875000 +0.106912 - +7 +32.125000 +0.114500 - +8 +27.125000 +0.097630 - - Density error is +0.000022029241 - - PW ALGORITHM --------------- ION=+21 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010617 - +2 +2.000000 +0.010405 - +3 +2.000000 +0.010373 - +4 +2.000000 +0.010365 - +5 +2.000000 +0.010388 - +6 +2.000000 +0.010360 - +7 +2.000000 +0.010347 - +8 +2.000000 +0.010369 - - Density error is +0.000001807441 - - PW ALGORITHM --------------- ION=+21 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011063 - +2 +2.375000 +0.011747 - +3 +2.250000 +0.011261 - +4 +2.500000 +0.012112 - +5 +2.250000 +0.011278 - +6 +2.625000 +0.012552 - +7 +3.000000 +0.013891 - +8 +2.375000 +0.011680 - - Density error is +0.000000029382 - - PW ALGORITHM --------------- ION=+21 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016299 - +2 +3.625000 +0.016094 - +3 +3.750000 +0.016491 - +4 +3.875000 +0.016919 - +5 +3.750000 +0.016502 - +6 +3.750000 +0.016462 - +7 +4.625000 +0.019557 - +8 +3.625000 +0.016026 - - Density error is +0.000000002371 - - PW ALGORITHM --------------- ION=+21 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013673 - +2 +2.875000 +0.013455 - +3 +2.875000 +0.013422 - +4 +4.125000 +0.017806 - +5 +3.000000 +0.013879 - +6 +3.875000 +0.016927 - +7 +3.000000 +0.013878 - +8 +2.875000 +0.013406 - - Density error is +0.000000000178 - - charge density convergence is achieved - final etot is -211.785114277951 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.597076 +0.443380 +0.097410 - Si2 +0.597076 -0.443380 -0.097410 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.145634 -2.476538 -12.011339 - -2.476538 +123.557627 +16.195950 - -12.011339 +16.195950 +124.041967 - -output Pressure for check! -Virtual Pressure is +124.075595 Kbar -Virial is +123.581743 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 21 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564066 (Rydberg) - NVT Temperature : +39.619227 (K) - NVT Kinetic energy : +0.000753 (Rydberg) - NVT Potential energy : -15.565913 (Rydberg) - maxForce : +0.000213 - maxStep : +0.014552 - MD_STEP SystemE Conserved DeltaE Temperature - +21 -7.782957 -7.782033 +0.000000 +19.004126 - - - -------------------------------------------- - !FINAL_ETOT_IS -211.7851142779510099 eV - -------------------------------------------- - - - - - - - |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- - total +35.575 15 +2.37 +100.00 % - Run_pw plane_wave_line +35.54 1 +35.54 +99.91 % - Run_MD_PW md_cells_pw +35.47 1 +35.47 +99.70 % - Potential init_pot +0.21 22 +0.01 +0.59 % - FFT FFT3D +21.26 126906 +0.00 +59.76 % - Potential v_of_rho +1.13 125 +0.01 +3.17 % - H_XC_pw v_xc +1.20 146 +0.01 +3.36 % - wavefunc wfcinit +0.97 22 +0.04 +2.73 % - pp_cell_vnl getvnl +0.46 1336 +0.00 +1.29 % - Hamilt_PW diagH_subspace +3.41 984 +0.00 +9.57 % - Hamilt_PW h_psi +24.29 52236 +0.00 +68.28 % - Hamilt_PW vloc +22.85 52236 +0.00 +64.24 % - Hamilt_PW vnl +1.29 52236 +0.00 +3.63 % - Hamilt_PW add_nonlocal_pp +0.75 52236 +0.00 +2.12 % - Run_MD_PW md_ions_pw +35.39 1 +35.39 +99.48 % - Electrons self_consistent +29.43 21 +1.40 +82.73 % - Electrons c_bands +25.56 103 +0.25 +71.86 % - Hamilt diagH_pw +25.14 824 +0.03 +70.67 % - Diago_CG diag +22.34 824 +0.03 +62.80 % - Charge sum_band +1.54 103 +0.01 +4.32 % - Charge mix_rho +0.20 103 +0.00 +0.57 % - Forces cal_force_nl +0.59 21 +0.03 +1.66 % - Stress_PW cal_stress +3.97 21 +0.19 +11.16 % - Stress_Func stress_ew +16.82 11 +1.53 +47.27 % - Force_Func stress_ew +16.82 11 +1.53 +47.27 % - Stress_Func stress_gga +0.11 21 +0.01 +0.31 % - Stress_Func stres_nl +3.76 21 +0.18 +10.57 % - ---------------------------------------------------------------------------------------- - - CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- - +5.1730 - ---------------------------------------------------------- - - Start Time : Fri Oct 15 14:37:16 2021 - Finish Time : Fri Oct 15 14:37:52 2021 - Total Time : 0 h 0 mins 36 secs diff --git a/tests/abacus.md/STRU b/tests/abacus.md/STRU index c3765e9bc..1152c0614 100644 --- a/tests/abacus.md/STRU +++ b/tests/abacus.md/STRU @@ -1,21 +1,32 @@ ATOMIC_SPECIES -Si 1.000 ./Si_ONCV_PBE-1.0.upf #Element, Mass, Pseudopotential +H 1.008 H_ONCV_PBE-1.0.upf +O 15.9994 O_ONCV_PBE-1.0.upf NUMERICAL_ORBITAL -./Si_gga_8au_60Ry_2s2p1d.orb +H_gga_8au_60Ry_2s1p.orb +O_gga_7au_60Ry_2s2p1d.orb + +NUMERICAL_DESCRIPTOR +jle.orb + LATTICE_CONSTANT -10.2 #Lattice constant +1 LATTICE_VECTORS -0.5 0.5 0.0 #Lattice vector 1 -0.5 0.0 0.5 #Lattice vector 2 -0.0 0.5 0.5 #Lattice vector 3 +28 0 0 +0 28 0 +0 0 28 ATOMIC_POSITIONS -Cartesian #Cartesian(Unit is LATTICE_CONSTANT) -Si #Name of element -0.0 #Magnetic for this element. -2 #Number of atoms -0.00 0.00 0.00 1 1 1 #x,y,z, move_x, move_y, move_z -0.241 0.255 0.251 1 1 1 +Cartesian + +H +0 +2 +-12.046787058887078 18.76558614676448 8.395247471328744 1 1 1 +-14.228868795885418 20.61549300274637 7.611989524516571 1 1 1 +O +0 +1 +-13.486789117423204 19.684192208418636 8.958321352749174 1 1 1 diff --git a/tests/abacus.md/Si_coord b/tests/abacus.md/Si_coord deleted file mode 100644 index fb8c5a8df..000000000 --- a/tests/abacus.md/Si_coord +++ /dev/null @@ -1,10 +0,0 @@ -0 0 0 -1.30082342 1.37638993 1.3547995 -5.35320953 2.72430477 2.68504527 -1.35126946 1.34726983 1.3286265 -2.70155326 2.69533522 5.35848569 -1.30969169 1.37268717 1.3150785 -2.66403555 0.02130293 2.64633444 -1.35284016 1.34443879 1.29061924 -2.70202696 2.69316139 5.32175227 -1.31985538 1.36795346 1.2771711 diff --git a/tests/abacus.md/Si_force b/tests/abacus.md/Si_force deleted file mode 100644 index b22dd3cc1..000000000 --- a/tests/abacus.md/Si_force +++ /dev/null @@ -1,10 +0,0 @@ --0.885363 0.500467 0.15024 -0.885363 -0.500467 -0.15024 -0.830073 -0.488698 -0.076368 --0.830073 0.488698 0.076368 --0.774114 0.493555 0.132287 -0.774114 -0.493555 -0.132287 -0.685454 -0.466777 -0.074732 --0.685454 0.466777 0.074732 --0.597076 0.44338 0.09741 -0.597076 -0.44338 -0.09741 diff --git a/tests/abacus.md/Si_virial b/tests/abacus.md/Si_virial deleted file mode 100644 index 8ee021799..000000000 --- a/tests/abacus.md/Si_virial +++ /dev/null @@ -1,15 +0,0 @@ --3.01924575 0.09342813 0.33227574 -0.09342813 -3.05301021 -0.59008156 -0.33227574 -0.59008156 -3.06760338 --3.02007615 -0.05764851 -0.32736857 --0.05764851 -3.0485708 0.55474523 --0.32736857 0.55474523 -3.06346952 --3.02121465 0.08230513 0.32783898 -0.08230513 -3.04371791 -0.51561023 -0.32783898 -0.51561023 -3.05814259 --3.02169395 -0.05491244 -0.31223515 --0.05491244 -3.03763085 0.45779192 --0.31223515 0.45779192 -3.05114849 --3.02170837 0.0607685 0.29473041 -0.0607685 -3.03181773 -0.39741107 -0.29473041 -0.39741107 -3.04370231 diff --git a/tests/abacus.md/water_coord b/tests/abacus.md/water_coord new file mode 100644 index 000000000..86266ed12 --- /dev/null +++ b/tests/abacus.md/water_coord @@ -0,0 +1,15 @@ +8.44207673 9.93032054 4.44257364 +7.2873688 10.90924909 4.02809139 +7.68006046 10.41642593 4.74053951 +8.45239543 9.92229615 4.45200117 +7.29575958 10.91312823 4.02455611 +7.67888171 10.41668709 4.74016828 +8.46343523 9.9140533 4.46015631 +7.30368632 10.91806892 4.01842335 +7.67768678 10.41689514 4.74004087 +8.47396587 9.90644051 4.46733013 +7.311549 10.92371331 4.00998943 +7.67652796 10.41701915 4.74012026 +8.48312789 9.89996318 4.47399619 +7.31947517 10.92982192 3.99979102 +7.67545136 10.41704238 4.7403428 \ No newline at end of file diff --git a/tests/abacus.md/water_force b/tests/abacus.md/water_force new file mode 100644 index 000000000..b6ac9021f --- /dev/null +++ b/tests/abacus.md/water_force @@ -0,0 +1,15 @@ +8.63308639e-01 -4.43254999e-01 -7.56985213e-01 +-2.00930882e-01 4.68126173e-01 -1.16095809e+00 +-6.62377758e-01 -2.48711741e-02 1.91794331e+00 +3.08447003e-01 -1.00596917e-01 -5.18349475e-01 +-2.19930471e-01 4.66062785e-01 -1.09553672e+00 +-8.85165314e-02 -3.65465868e-01 1.61388619e+00 +-4.21531964e-01 4.78003484e-01 -6.02669271e-01 +2.65214978e-01 7.64070864e-02 -9.63824372e-01 +1.56316986e-01 -5.54410570e-01 1.56649364e+00 +-5.43198631e-01 4.57161184e-01 -2.06821527e-01 +2.27096399e-02 2.11549052e-01 -7.58980258e-01 +5.20488991e-01 -6.68710236e-01 9.65801785e-01 +-8.12329959e-01 5.87918500e-01 9.41318509e-04 +3.98264319e-02 1.00785737e-01 -4.50166048e-01 +7.72503527e-01 -6.88704237e-01 4.49224729e-01 \ No newline at end of file diff --git a/tests/abacus.md/water_virial b/tests/abacus.md/water_virial new file mode 100644 index 000000000..b707c9aeb --- /dev/null +++ b/tests/abacus.md/water_virial @@ -0,0 +1,15 @@ +6.95335395e-01 -5.08824989e-01 -1.09549510e-01 +-5.08824989e-01 4.04209230e-01 -2.00245250e-01 +-1.09549510e-01 -2.00245250e-01 9.66902194e-01 +3.14181369e-01 -2.55243046e-01 3.04054313e-04 +-2.55243046e-01 2.42582203e-01 -2.84883570e-01 +3.04054313e-04 -2.84883570e-01 9.28206167e-01 +-1.85150181e-01 1.05732829e-01 4.21143979e-02 +1.05732829e-01 -2.56256968e-02 -2.78554734e-01 +4.21143979e-02 -2.78554734e-01 7.64038483e-01 +-5.03355372e-01 3.34823165e-01 6.91010112e-02 +3.34823165e-01 -1.99581996e-01 -2.60526766e-01 +6.91010112e-02 -2.60526766e-01 6.12151015e-01 +-8.20817678e-01 5.82037040e-01 3.83817596e-02 +5.82037040e-01 -4.11511524e-01 -1.70276239e-01 +3.83817596e-02 -1.70276239e-01 3.83953980e-01 \ No newline at end of file diff --git a/tests/test_abacus_md.py b/tests/test_abacus_md.py index 1ce7cf8d0..2ed61a994 100644 --- a/tests/test_abacus_md.py +++ b/tests/test_abacus_md.py @@ -9,54 +9,52 @@ class TestABACUSMD: def test_atom_names(self) : - self.assertEqual(self.system_Si.data['atom_names'], ['Si']) - #self.assertEqual(self.system_h2o.data['atom_names'], ['O','H']) + self.assertEqual(self.system_water.data['atom_names'], ['H', 'O']) def test_atom_numbs(self) : - self.assertEqual(self.system_Si.data['atom_numbs'], [2]) - #self.assertEqual(self.system_h2o.data['atom_numbs'], [64,128]) + self.assertEqual(self.system_water.data['atom_numbs'], [2, 1]) def test_atom_types(self) : - ref_type = [0, 0] + ref_type = [0, 0, 1] ref_type = np.array(ref_type) for ii in range(ref_type.shape[0]) : - self.assertEqual(self.system_Si.data['atom_types'][ii], ref_type[ii]) + self.assertEqual(self.system_water.data['atom_types'][ii], ref_type[ii]) def test_cell(self) : - cell = bohr2ang * 10.2 * np.array([[0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]]) - for idx in range(np.shape(self.system_Si.data['cells'])[0]): + cell = bohr2ang * 28 * np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]) + for idx in range(np.shape(self.system_water.data['cells'])[0]): for ii in range(cell.shape[0]) : for jj in range(cell.shape[1]) : - self.assertAlmostEqual(self.system_Si.data['cells'][idx][ii][jj], cell[ii][jj]) + self.assertAlmostEqual(self.system_water.data['cells'][idx][ii][jj], cell[ii][jj]) def test_coord(self) : - fp = open('abacus.md/Si_coord') + fp = open('abacus.md/water_coord') coord = [] for ii in fp : coord.append([float(jj) for jj in ii.split()]) coord = np.array(coord) - coord = coord.reshape([5, 2, 3]) + coord = coord.reshape([5, 3, 3]) for ii in range(coord.shape[0]) : for jj in range(coord.shape[1]) : for kk in range(coord.shape[2]): - self.assertAlmostEqual(self.system_Si.data['coords'][ii][jj][kk], coord[ii][jj][kk]) + self.assertAlmostEqual(self.system_water.data['coords'][ii][jj][kk], coord[ii][jj][kk]) fp.close() def test_force(self) : - fp = open('abacus.md/Si_force') + fp = open('abacus.md/water_force') force = [] for ii in fp : force.append([float(jj) for jj in ii.split()]) force = np.array(force) - force = force.reshape([5, 2, 3]) + force = force.reshape([5, 3, 3]) for ii in range(force.shape[0]) : for jj in range(force.shape[1]) : for kk in range(force.shape[2]): - self.assertAlmostEqual(self.system_Si.data['forces'][ii][jj][kk], force[ii][jj][kk]) + self.assertAlmostEqual(self.system_water.data['forces'][ii][jj][kk], force[ii][jj][kk]) fp.close() def test_virial(self) : - fp = open('abacus.md/Si_virial') + fp = open('abacus.md/water_virial') virial = [] for ii in fp : virial.append([float(jj) for jj in ii.split()]) @@ -65,21 +63,20 @@ def test_virial(self) : for ii in range(virial.shape[0]) : for jj in range(virial.shape[1]) : for kk in range(virial.shape[2]) : - self.assertAlmostEqual(self.system_Si.data['virials'][ii][jj][kk], virial[ii][jj][kk]) + self.assertAlmostEqual(self.system_water.data['virials'][ii][jj][kk], virial[ii][jj][kk]) fp.close() def test_energy(self) : - ref_energy = np.array([-211.77183266, -211.7739761 , -211.77713677, -211.78079673, - -211.78511428]) + ref_energy = np.array([-466.69285117, -466.69929051, -466.69829826, -466.70364664, + -466.6976083]) for ii in range(5): - self.assertAlmostEqual(self.system_Si.data['energies'][ii], ref_energy[ii]) + self.assertAlmostEqual(self.system_water.data['energies'][ii], ref_energy[ii]) class TestABACUSMDLabeledOutput(unittest.TestCase, TestABACUSMD): def setUp(self): - self.system_Si = dpdata.LabeledSystem('abacus.md',fmt='abacus/md') - # self.system_h2o = dpdata.LabeledSystem('qe.scf/02.out',fmt='qe/pw/scf') + self.system_water = dpdata.LabeledSystem('abacus.md',fmt='abacus/md') if __name__ == '__main__':