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adapt abacus/md interface to MD output without stress calculation. #301

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Merged
AnguseZhang merged 4 commits into from
Jun 11, 2022
Merged

adapt abacus/md interface to MD output without stress calculation. #301

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e12271d
adapt abacus/md interface to MD output without stress calculation.
Jun 8, 2022
61e1040
add unit test for abacus md without stress output.
Jun 9, 2022
a5e42a7
Add files via upload
Liu-RX Jun 9, 2022
f939712
add assertion failed reason for abacus/md interface
Jun 11, 2022
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28 changes: 21 additions & 7 deletions dpdata/abacus/md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,17 @@ def get_coord_dump_freq(inlines):
def get_coords_from_dump(dumplines, natoms):
nlines = len(dumplines)
total_natoms = sum(natoms)
nframes_dump = int(nlines/(total_natoms + 13))

calc_stress = False
if "VIRIAL" in dumplines[6]:
calc_stress = True
else:
assert("POSITIONS" in dumplines[6] and "FORCE" in dumplines[6]), "keywords 'POSITIONS' and 'FORCE' cannot be found in the 6th line. Please check."
nframes_dump = -1

@njzjz njzjz Jun 11, 2022

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This line is useless.

@Liu-RX Liu-RX Jun 11, 2022

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Hi Jinzhe. I think the line is helpful in recognizing the keywords are in the right place of the file, so I kept the lines.

@AnguseZhang AnguseZhang Jun 11, 2022

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If you delete nframes_dump, it will still be defined in the successive conditional lines. But I think keeping this line is also okay.

if calc_stress:
nframes_dump = int(nlines/(total_natoms + 13))
else:
nframes_dump = int(nlines/(total_natoms + 9))
assert(nframes_dump > 0), "Number of lines in MD_dump file = %d. Number of atoms = %d. The MD_dump file is incomplete."%(nlines, total_natoms)
cells = np.zeros([nframes_dump, 3, 3])
stresses = np.zeros([nframes_dump, 3, 3])
forces = np.zeros([nframes_dump, total_natoms, 3])
Expand All @@ -47,12 +56,17 @@ def get_coords_from_dump(dumplines, natoms):
# 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:]])
if calc_stress:
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:]])
if calc_stress:
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:]])
else:
coords[iframe, iat] = np.array([float(i) for i in re.split('\s+', dumplines[iline+7+iat])[-6:-3]])*celldm
forces[iframe, iat] = np.array([float(i) for i in re.split('\s+', dumplines[iline+7+iat])[-3:]])
iframe += 1
assert(iframe == nframes_dump)
assert(iframe == nframes_dump), "iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump."%(iframe, nframes_dump)
cells *= bohr2ang
coords *= bohr2ang
stresses *= kbar2evperang3
Expand All @@ -66,7 +80,7 @@ def get_energy(outlines, ndump, dump_freq):
if nenergy%dump_freq == 0:
energy.append(float(line.split()[-2]))
nenergy+=1
assert(ndump == len(energy))
assert(ndump == len(energy)), "Number of total energies in running_md.log = %d. Number of frames in MD_dump = %d. Please check."%(len(energy), ndump)
energy = np.array(energy)
return energy

Expand Down
27 changes: 27 additions & 0 deletions tests/abacus.md.nostress/INPUT
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Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
INPUT_PARAMETERS
#Parameters (General)
suffix autotest
pseudo_dir ./
ntype 1
nbands 8
calculation md

#Parameters (Accuracy)
ecutwfc 20
scf_nmax 20

basis_type pw
md_nstep 3

#cal_stress 1
stress_thr 1e-6
cal_force 1
force_thr_ev 1.0e-3

ks_solver cg
mixing_type pulay
mixing_beta 0.7

md_type -1
md_dt 1
md_tfirst 0
44 changes: 44 additions & 0 deletions tests/abacus.md.nostress/OUT.autotest/MD_dump
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Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
MDSTEP: 0
LATTICE_CONSTANT: 10.200000000000
LATTICE_VECTORS
0.500000000000 0.500000000000 0.000000000000
0.500000000000 0.000000000000 0.500000000000
0.000000000000 0.500000000000 0.500000000000
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 Si 0.000000000000 0.000000000000 0.000000000000 -0.885362725259 0.500467424429 0.150239620221
1 Si 0.241000000000 0.255000000000 0.250999999999 0.885362725259 -0.500467424429 -0.150239620221


MDSTEP: 1
LATTICE_CONSTANT: 10.200000000000
LATTICE_VECTORS
0.500000000000 0.500000000000 0.000000000000
0.500000000000 0.000000000000 0.500000000000
0.000000000000 0.500000000000 0.500000000000
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 Si 0.999208682339 0.500447306737 0.500134280856 -0.728804779648 0.408578746723 0.107042476463
1 Si 0.241791317661 0.254552693263 0.250865719143 0.728804779648 -0.408578746723 -0.107042476463


MDSTEP: 2
LATTICE_CONSTANT: 10.200000000000
LATTICE_VECTORS
0.500000000000 0.500000000000 0.000000000000
0.500000000000 0.000000000000 0.500000000000
0.000000000000 0.500000000000 0.500000000000
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 Si 0.997114226602 0.501624803733 0.500458153134 -0.316038867402 0.171613491764 0.014802659803
1 Si 0.243885773398 0.253375196267 0.250541846865 0.316038867402 -0.171613491764 -0.014802659803


MDSTEP: 3
LATTICE_CONSTANT: 10.200000000000
LATTICE_VECTORS
0.500000000000 0.500000000000 0.000000000000
0.500000000000 0.000000000000 0.500000000000
0.000000000000 0.500000000000 0.500000000000
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 Si 0.994451593844 0.503106810892 0.500786060548 0.204324467775 -0.117398116295 -0.052955519257
1 Si 0.246548406156 0.251893189108 0.250213939451 -0.204324467775 0.117398116295 0.052955519257


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