From 39462757c46e0d8cfea8830d68aa4f9a84e60d58 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sat, 21 May 2022 18:31:34 -0400 Subject: [PATCH] fix reading SQM minimization output Before, only single-point calculation output is supported. --- dpdata/amber/sqm.py | 8 +- tests/amber/sqm_opt.out | 771 ++++++++++++++++++++++++++++++++++++++++ tests/test_amber_sqm.py | 16 + 3 files changed, 794 insertions(+), 1 deletion(-) create mode 100644 tests/amber/sqm_opt.out diff --git a/dpdata/amber/sqm.py b/dpdata/amber/sqm.py index 62f7424e9..557bbd6ce 100644 --- a/dpdata/amber/sqm.py +++ b/dpdata/amber/sqm.py @@ -25,15 +25,18 @@ def parse_sqm_out(fname): for line in f: if line.startswith(" Total SCF energy"): energy = float(line.strip().split()[-2]) - energies.append(energy) + energies = [energy] elif line.startswith(" Atom Element Mulliken Charge"): flag = READ_CHARGE + charges = [] elif line.startswith(" Total Mulliken Charge"): flag = START elif line.startswith(" Final Structure"): flag = READ_COORDS_START + coords = [] elif line.startswith("QMMM: Forces on QM atoms"): flag = READ_FORCES + forces = [] elif flag == READ_CHARGE: ls = line.strip().split() atom_symbols.append(ls[-2]) @@ -46,6 +49,9 @@ def parse_sqm_out(fname): flag = START elif flag == READ_FORCES: ll = line.strip() + if not ll.startswith("QMMM: Atm "): + flag = START + continue forces.append([float(ll[-60:-40]), float(ll[-40:-20]), float(ll[-20:])]) if len(forces) == len(charges): flag = START diff --git a/tests/amber/sqm_opt.out b/tests/amber/sqm_opt.out new file mode 100644 index 000000000..6e32002bd --- /dev/null +++ b/tests/amber/sqm_opt.out @@ -0,0 +1,771 @@ + -------------------------------------------------------- + AMBER SQM VERSION 19 + + By + Ross C. Walker, Michael F. Crowley, Scott Brozell, + Tim Giese, Andreas W. Goetz, + Tai-Sung Lee and David A. Case + + -------------------------------------------------------- + + +-------------------------------------------------------------------------------- + QM CALCULATION INFO +-------------------------------------------------------------------------------- + +| QMMM: Citation for AMBER QMMM Run: +| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008 + +| QMMM: DFTB Calculation - Additional citation for AMBER DFTB QMMM Run: +| QMMM: Seabra, G.M., Walker, R.C. et al., J. PHYS. CHEM. A., 111, 5655, (2007) + +| QMMM: DFTB3 - Additional citation to follow. Implementation by: +| QMMM: A.W. Goetz +| QMMM: +| QMMM: DFTB3 method citation: +| QMMM: M. Gaus, Q. Cui, M. Elstner, J. CHEM. THEORY COMPUT. 7, 931 (2011) +| QMMM: +| QMMM: DFTB3 dispersion correction [D3(BJ)] and halogen correction not available. + +| QMMM: Please cite also the appropriate references for the DFTB parameters +| QMMM: that you are using (see the manual and www.dftb.org). + + +QMMM: SINGLET STATE CALCULATION +QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 4 + +| QMMM: *** SCF convergence criteria *** +| QMMM: Energy change : 0.1D-07 kcal/mol +| QMMM: Error matrix |FP-PF| : 0.1D+00 au +| QMMM: Density matrix change : 0.5D-05 +| QMMM: Maximum number of SCF cycles : 1000 + DFTB: Number of atom types = 2 + + Parameter files: + TYP (AT) TYP (AT) SK integral FILE +| 1 1 (C ) 1 (C ) /usr/local/amber20/dat/slko/3ob-3-1/C-C.skf +| 2 1 (C ) 2 (H ) /usr/local/amber20/dat/slko/3ob-3-1/C-H.skf +| 3 2 (H ) 1 (C ) /usr/local/amber20/dat/slko/3ob-3-1/H-C.skf +| 4 2 (H ) 2 (H ) /usr/local/amber20/dat/slko/3ob-3-1/H-H.skf + +QMMM: Hubbard Derivatives dU/dq: +QMMM: C -0.149200 +QMMM: H -0.185700 + +QMMM: zeta = 4.000000 + + QMMM: QM Region Cartesian Coordinates (*=link atom) + QMMM: QM_NO. MM_NO. ATOM X Y Z + QMMM: 1 1 C -0.0221 0.0032 0.0165 + QMMM: 2 2 H -0.6690 0.8894 -0.1009 + QMMM: 3 3 H -0.3778 -0.8578 -0.5883 + QMMM: 4 4 H 0.0964 -0.3151 1.0638 + QMMM: 5 5 H 0.9725 0.2803 -0.3911 + +-------------------------------------------------------------------------------- + RESULTS +-------------------------------------------------------------------------------- + + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C -0.0221000000 0.0032000000 0.0165000000 0.0000000000 + QMMM SCC-DFTB: 2 2 1 1 H -0.6690000000 0.8894000000 -0.1009000000 0.0000000000 + QMMM SCC-DFTB: 3 2 1 1 H -0.3778000000 -0.8578000000 -0.5883000000 0.0000000000 + QMMM SCC-DFTB: 4 2 1 1 H 0.0964000000 -0.3151000000 1.0638000000 0.0000000000 + QMMM SCC-DFTB: 5 2 1 1 H 0.9725000000 0.2803000000 -0.3911000000 0.0000000000 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.157799880131646 + QMMM SCC-DFTB: 2 -3.157824613290581 -0.000024733158935 0.298293766328793 1 1 C -0.37250 + QMMM SCC-DFTB: 3 -3.158199563935489 -0.000374950644908 0.019934591031811 1 1 C -0.39847 + QMMM SCC-DFTB: 4 -3.158238966380289 -0.000039402444800 0.002476750818148 1 1 C -0.40133 + QMMM SCC-DFTB: 5 -3.158255573884495 -0.000016607504205 0.004585404872750 1 1 C -0.40251 + QMMM SCC-DFTB: 6 -3.158245092771366 0.000010481113129 0.000107585599371 1 1 C -0.40174 + QMMM SCC-DFTB: 7 -3.158244836495692 0.000000256275674 0.000002411826609 1 1 C -0.40172 + QMMM SCC-DFTB: 8 -3.158244842549473 -0.000000006053781 0.000000199663518 1 1 C -0.40172 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 8 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -85.935842165771 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.924790869738 + QMMM SCC-DFTB: Total Energy (eV) = -87.860633035509 + QMMM SCC-DFTB: SCF Energy (eV) = -18.131741202909 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.158244842549 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.070738363460 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.228983206009 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.666363146009 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -418.13608388028837 KCal/mol, -1749.48137495512651 KJ/mol +QMMM: +QMMM: Electronic energy = -85.93584217 eV ( -1981.76645618 KCal/mol) +QMMM: Repulsive energy = -1.92479087 eV ( -44.38760225 KCal/mol) +QMMM: Total energy = -87.86063304 eV ( -2026.15405843 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -13.74670327739973 3.65547862388900 13.81483034563851 +QMMM: Atm 2: -4.90340977577246 16.35088467587560 -5.20621249045626 +QMMM: Atm 3: -1.43273040245665 -17.63544875270559 -11.91662605007330 +QMMM: Atm 4: 4.44538283013336 -7.38377343857182 12.75287244204118 +QMMM: Atm 5: 15.63746062570429 5.01285889151487 -9.44486424761330 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C -0.0220999687 0.0031999917 0.0164999685 -0.4017199086 + QMMM SCC-DFTB: 2 2 1 1 H -0.6689999888 0.8893999627 -0.1008999881 0.1047408987 + QMMM SCC-DFTB: 3 2 1 1 H -0.3777999967 -0.8577999598 -0.5882999728 0.0991061487 + QMMM SCC-DFTB: 4 2 1 1 H 0.0963999899 -0.3150999832 1.0637999709 0.1043123572 + QMMM SCC-DFTB: 5 2 1 1 H 0.9724999643 0.2802999886 -0.3910999785 0.0935605041 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.158244872256237 + QMMM SCC-DFTB: 2 -3.158244872254534 0.000000000001703 0.000000015122551 4 4 H 0.10431 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -85.935842974046 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.924790223407 + QMMM SCC-DFTB: Total Energy (eV) = -87.860633197453 + QMMM SCC-DFTB: SCF Energy (eV) = -18.131741364853 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.158244872255 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.070738339706 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.228983211961 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.666363151961 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -418.13608761487853 KCal/mol, -1749.48139058065181 KJ/mol +QMMM: +QMMM: Electronic energy = -85.93584297 eV ( -1981.76647482 KCal/mol) +QMMM: Repulsive energy = -1.92479022 eV ( -44.38758734 KCal/mol) +QMMM: Total energy = -87.86063320 eV ( -2026.15406217 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -13.74666278262608 3.65546521339185 13.81478479550825 +QMMM: Atm 2: -4.90340646058408 16.35087377436513 -5.20620722220688 +QMMM: Atm 3: -1.43272261896924 -17.63541726762958 -11.91660188136875 +QMMM: Atm 4: 4.44537812583215 -7.38376888783980 12.75286665628583 +QMMM: Atm 5: 15.63741373622763 5.01284716771441 -9.44484234833637 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C -0.0221000121 0.0032000084 0.0165000217 -0.4017199009 + QMMM SCC-DFTB: 2 2 1 1 H -0.6689999826 0.8893999415 -0.1008999849 0.1047408876 + QMMM SCC-DFTB: 3 2 1 1 H -0.3778000082 -0.8577999755 -0.5882999891 0.0991061590 + QMMM SCC-DFTB: 4 2 1 1 H 0.0963999875 -0.3150999729 1.0637999491 0.1043123380 + QMMM SCC-DFTB: 5 2 1 1 H 0.9725000154 0.2802999985 -0.3910999967 0.0935605164 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.158244864097563 + QMMM SCC-DFTB: 2 -3.158244864091829 0.000000000005735 0.000000028544296 5 5 H 0.09356 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -85.935842751939 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.924790352857 + QMMM SCC-DFTB: Total Energy (eV) = -87.860633104795 + QMMM SCC-DFTB: SCF Energy (eV) = -18.131741272195 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.158244864092 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.070738344464 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.228983208556 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.666363148556 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -418.13608547809997 KCal/mol, -1749.48138164037027 KJ/mol +QMMM: +QMMM: Electronic energy = -85.93584275 eV ( -1981.76646970 KCal/mol) +QMMM: Repulsive energy = -1.92479035 eV ( -44.38759033 KCal/mol) +QMMM: Total energy = -87.86063310 eV ( -2026.15406003 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -13.74674292408972 3.65549549628298 13.81488140458653 +QMMM: Atm 2: -4.90338368522172 16.35084405392652 -5.20620836094378 +QMMM: Atm 3: -1.43272964586336 -17.63544295426037 -11.91662475897387 +QMMM: Atm 4: 4.44537778375399 -7.38375816312764 12.75282322394532 +QMMM: Atm 5: 15.63747847251340 5.01286156692956 -9.44487150789251 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C -0.0220999770 0.0031999942 0.0164999786 -0.4017198929 + QMMM SCC-DFTB: 2 2 1 1 H -0.6690000286 0.8893999644 -0.1008999763 0.1047409081 + QMMM SCC-DFTB: 3 2 1 1 H -0.3778000356 -0.8577999896 -0.5883000054 0.0991061407 + QMMM SCC-DFTB: 4 2 1 1 H 0.0963999854 -0.3150999728 1.0638000028 0.1043123640 + QMMM SCC-DFTB: 5 2 1 1 H 0.9725000558 0.2803000039 -0.3910999998 0.0935604801 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.158244838402994 + QMMM SCC-DFTB: 2 -3.158244838395710 0.000000000007284 0.000000023300674 4 4 H 0.10431 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -85.935842052747 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.924790997617 + QMMM SCC-DFTB: Total Energy (eV) = -87.860633050364 + QMMM SCC-DFTB: SCF Energy (eV) = -18.131741217764 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.158244838396 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.070738368159 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.228983206555 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.666363146555 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -418.13608422286637 KCal/mol, -1749.48137638847288 KJ/mol +QMMM: +QMMM: Electronic energy = -85.93584205 eV ( -1981.76645358 KCal/mol) +QMMM: Repulsive energy = -1.92479100 eV ( -44.38760520 KCal/mol) +QMMM: Total energy = -87.86063305 eV ( -2026.15405877 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -13.74670305475924 3.65547229171135 13.81481909316784 +QMMM: Atm 2: -4.90341744044170 16.35087993595888 -5.20620701223694 +QMMM: Atm 3: -1.43273826196118 -17.63544523659553 -11.91662485212175 +QMMM: Atm 4: 4.44537952259198 -7.38376958855279 12.75287923818410 +QMMM: Atm 5: 15.63747923478301 5.01286259730783 -9.44486646623504 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C -0.0022758867 -0.0007767586 -0.0007109555 -0.4017198684 + QMMM SCC-DFTB: 2 2 1 1 H -0.6673769496 0.8463624077 -0.0844628839 0.1047408826 + QMMM SCC-DFTB: 3 2 1 1 H -0.3882629741 -0.8284725465 -0.5733587230 0.0991061497 + QMMM SCC-DFTB: 4 2 1 1 H 0.0840834583 -0.2923013588 1.0377587851 0.1043123345 + QMMM SCC-DFTB: 5 2 1 1 H 0.9738324351 0.2751884580 -0.3792280081 0.0935605016 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177019277204838 + QMMM SCC-DFTB: 2 -3.177025052002878 -0.000005774798040 0.010493789293413 1 1 C -0.41474 + QMMM SCC-DFTB: 3 -3.177047239463107 -0.000022187460229 0.002204125798446 1 1 C -0.41618 + QMMM SCC-DFTB: 4 -3.177053122189775 -0.000005882726668 0.000021626035352 2 2 H 0.10441 + QMMM SCC-DFTB: 5 -3.177053178549945 -0.000000056360170 0.000001222939759 2 2 H 0.10441 + QMMM SCC-DFTB: 6 -3.177053178489194 0.000000000060751 0.000000018760599 1 1 C -0.41657 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 6 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.447616986691 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.471967370268 + QMMM SCC-DFTB: Total Energy (eV) = -87.919584356959 + QMMM SCC-DFTB: SCF Energy (eV) = -18.190692524359 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177053178489 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.054096558996 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231149737485 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668529677485 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.49556030423253 KCal/mol, -1755.16942431290886 KJ/mol +QMMM: +QMMM: Electronic energy = -86.44761699 eV ( -1993.56849533 KCal/mol) +QMMM: Repulsive energy = -1.47196737 eV ( -33.94503953 KCal/mol) +QMMM: Total energy = -87.91958436 eV ( -2027.51353486 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -3.00001738071813 -1.50619543749513 -1.58741102759545 +QMMM: Atm 2: 0.60135963409961 0.36993708543853 0.02617975416810 +QMMM: Atm 3: 1.00751030160294 0.98592419104974 1.13885513088302 +QMMM: Atm 4: 0.13675393072060 -0.51889044079648 1.02882655685741 +QMMM: Atm 5: 1.25439351430015 0.66922460179871 -0.60645041442821 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C -0.0022758254 -0.0007767336 -0.0007109343 -0.4165722368 + QMMM SCC-DFTB: 2 2 1 1 H -0.6673769737 0.8463623871 -0.0844628744 0.1044109119 + QMMM SCC-DFTB: 3 2 1 1 H -0.3882630080 -0.8284725620 -0.5733587476 0.1048882360 + QMMM SCC-DFTB: 4 2 1 1 H 0.0840834501 -0.2923013382 1.0377587695 0.1038385532 + QMMM SCC-DFTB: 5 2 1 1 H 0.9738324400 0.2751884484 -0.3792279986 0.1034345357 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177053176423371 + QMMM SCC-DFTB: 2 -3.177053176424210 -0.000000000000839 0.000000021241782 5 5 H 0.10343 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.447616930503 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.471967444611 + QMMM SCC-DFTB: Total Energy (eV) = -87.919584375114 + QMMM SCC-DFTB: SCF Energy (eV) = -18.190692542514 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177053176424 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.054096561728 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231149738152 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668529678152 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.49556072291301 KCal/mol, -1755.16942606466819 KJ/mol +QMMM: +QMMM: Electronic energy = -86.44761693 eV ( -1993.56849403 KCal/mol) +QMMM: Repulsive energy = -1.47196744 eV ( -33.94504124 KCal/mol) +QMMM: Total energy = -87.91958438 eV ( -2027.51353527 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -2.99993072311282 -1.50614849359069 -1.58736044544401 +QMMM: Atm 2: 0.60134391066191 0.36993942396946 0.02617856069717 +QMMM: Atm 3: 1.00748094020025 0.98587971470655 1.13882119827186 +QMMM: Atm 4: 0.13674581727437 -0.51888280486258 1.02879998530180 +QMMM: Atm 5: 1.25436005443588 0.66921216009831 -0.60643929883291 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C -0.0022758759 -0.0007767626 -0.0007109613 -0.4165722380 + QMMM SCC-DFTB: 2 2 1 1 H -0.6673769734 0.8463623560 -0.0844628783 0.1044109015 + QMMM SCC-DFTB: 3 2 1 1 H -0.3882629907 -0.8284725004 -0.5733587378 0.1048882103 + QMMM SCC-DFTB: 4 2 1 1 H 0.0840834733 -0.2923013234 1.0377587795 0.1038385635 + QMMM SCC-DFTB: 5 2 1 1 H 0.9738324498 0.2751884322 -0.3792279874 0.1034345627 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177053189902282 + QMMM SCC-DFTB: 2 -3.177053189906454 -0.000000000004173 0.000000029572285 3 3 H 0.10489 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.447617297355 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.471967063523 + QMMM SCC-DFTB: Total Energy (eV) = -87.919584360878 + QMMM SCC-DFTB: SCF Energy (eV) = -18.190692528278 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177053189906 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.054096547722 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231149737629 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668529677629 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.49556039461277 KCal/mol, -1755.16942469105993 KJ/mol +QMMM: +QMMM: Electronic energy = -86.44761730 eV ( -1993.56850249 KCal/mol) +QMMM: Repulsive energy = -1.47196706 eV ( -33.94503245 KCal/mol) +QMMM: Total energy = -87.91958436 eV ( -2027.51353495 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -3.00001595789464 -1.50619959497283 -1.58741808638720 +QMMM: Atm 2: 0.60135965944853 0.36992131728738 0.02618177329187 +QMMM: Atm 3: 1.00751092479538 0.98594231266698 1.13885924141731 +QMMM: Atm 4: 0.13675562187275 -0.51888230503968 1.02882105346303 +QMMM: Atm 5: 1.25438975749003 0.66921826988072 -0.60644398225300 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C -0.0022759240 -0.0007767665 -0.0007109443 -0.4165722482 + QMMM SCC-DFTB: 2 2 1 1 H -0.6673769688 0.8463624208 -0.0844629104 0.1044109120 + QMMM SCC-DFTB: 3 2 1 1 H -0.3882629652 -0.8284725266 -0.5733587547 0.1048882478 + QMMM SCC-DFTB: 4 2 1 1 H 0.0840835104 -0.2923013583 1.0377588146 0.1038385508 + QMMM SCC-DFTB: 5 2 1 1 H 0.9738324306 0.2751884323 -0.3792279905 0.1034345376 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177053171661357 + QMMM SCC-DFTB: 2 -3.177053171655763 0.000000000005594 0.000000010752099 5 5 H 0.10343 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.447616800753 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.471967554219 + QMMM SCC-DFTB: Total Energy (eV) = -87.919584354973 + QMMM SCC-DFTB: SCF Energy (eV) = -18.190692522373 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177053171656 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.054096565756 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231149737412 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668529677412 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.49556025843816 KCal/mol, -1755.16942412130538 KJ/mol +QMMM: +QMMM: Electronic energy = -86.44761680 eV ( -1993.56849104 KCal/mol) +QMMM: Repulsive energy = -1.47196755 eV ( -33.94504377 KCal/mol) +QMMM: Total energy = -87.91958435 eV ( -2027.51353481 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -3.00004968153394 -1.50620963619432 -1.58741778817088 +QMMM: Atm 2: 0.60135657004798 0.36994265717245 0.02617394714159 +QMMM: Atm 3: 1.00751788058786 0.98593536590786 1.13885373849680 +QMMM: Atm 4: 0.13676701341870 -0.51889254828514 1.02884259812090 +QMMM: Atm 5: 1.25440821726414 0.66922416139912 -0.60645249570357 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C 0.0000038338 -0.0000741137 -0.0000915666 -0.4165722357 + QMMM SCC-DFTB: 2 2 1 1 H -0.6690925881 0.8440618468 -0.0841048801 0.1044109150 + QMMM SCC-DFTB: 3 2 1 1 H -0.3899330263 -0.8274220054 -0.5748810102 0.1048882424 + QMMM SCC-DFTB: 4 2 1 1 H 0.0845718862 -0.2904408216 1.0372016233 0.1038385542 + QMMM SCC-DFTB: 5 2 1 1 H 0.9744495465 0.2738752702 -0.3781262149 0.1034345240 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177297107065937 + QMMM SCC-DFTB: 2 -3.177297189242046 -0.000000082176109 0.000714476993429 5 5 H 0.10434 + QMMM SCC-DFTB: 3 -3.177297448974965 -0.000000259732919 0.000050374225117 1 1 C -0.41677 + QMMM SCC-DFTB: 4 -3.177297583444879 -0.000000134469914 0.000000664777074 1 1 C -0.41678 + QMMM SCC-DFTB: 5 -3.177297585243204 -0.000000001798325 0.000000010687417 4 4 H 0.10417 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 5 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.454267294468 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.465661705715 + QMMM SCC-DFTB: Total Energy (eV) = -87.919929000182 + QMMM SCC-DFTB: SCF Energy (eV) = -18.191037167582 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177297585243 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.053864818292 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231162403535 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668542343535 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.50350812161315 KCal/mol, -1755.20267798082955 KJ/mol +QMMM: +QMMM: Electronic energy = -86.45426729 eV ( -1993.72185808 KCal/mol) +QMMM: Repulsive energy = -1.46566171 eV ( -33.79962460 KCal/mol) +QMMM: Total energy = -87.91992900 eV ( -2027.52148267 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -0.08397438585120 -0.11992372445546 -0.11648100404662 +QMMM: Atm 2: 0.02413338666108 -0.01213651509183 0.01920691201260 +QMMM: Atm 3: 0.04594261530503 0.10271287370538 0.09299635501682 +QMMM: Atm 4: -0.02000842001580 -0.00089167325386 0.01917324403620 +QMMM: Atm 5: 0.03390680653361 0.03023903909095 -0.01489550500940 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C 0.0000038243 -0.0000740764 -0.0000915287 -0.4167784643 + QMMM SCC-DFTB: 2 2 1 1 H -0.6690926075 0.8440618473 -0.0841048975 0.1041805592 + QMMM SCC-DFTB: 3 2 1 1 H -0.3899330395 -0.8274220238 -0.5748810590 0.1042383015 + QMMM SCC-DFTB: 4 2 1 1 H 0.0845719235 -0.2904408174 1.0372016385 0.1041707783 + QMMM SCC-DFTB: 5 2 1 1 H 0.9744495513 0.2738752466 -0.3781262018 0.1041888253 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177297572848879 + QMMM SCC-DFTB: 2 -3.177297572844566 0.000000000004313 0.000000020485338 3 3 H 0.10424 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.454266957101 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.465662044402 + QMMM SCC-DFTB: Total Energy (eV) = -87.919929001502 + QMMM SCC-DFTB: SCF Energy (eV) = -18.191037168902 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177297572845 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.053864830739 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231162403583 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668542343583 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.50350815205553 KCal/mol, -1755.20267810820042 KJ/mol +QMMM: +QMMM: Electronic energy = -86.45426696 eV ( -1993.72185030 KCal/mol) +QMMM: Repulsive energy = -1.46566204 eV ( -33.79963241 KCal/mol) +QMMM: Total energy = -87.91992900 eV ( -2027.52148270 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -0.08396941860273 -0.11985835095379 -0.11642882888525 +QMMM: Atm 2: 0.02413760202554 -0.01214907360599 0.01920165485925 +QMMM: Atm 3: 0.04592229065449 0.10266729765707 0.09295742713355 +QMMM: Atm 4: -0.02000172847949 -0.00089224660803 0.01916687245340 +QMMM: Atm 5: 0.03391125450313 0.03023237989853 -0.01489712556091 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C 0.0000038614 -0.0000741309 -0.0000915578 -0.4167784546 + QMMM SCC-DFTB: 2 2 1 1 H -0.6690926261 0.8440618880 -0.0841049009 0.1041805702 + QMMM SCC-DFTB: 3 2 1 1 H -0.3899330240 -0.8274220040 -0.5748810378 0.1042382755 + QMMM SCC-DFTB: 4 2 1 1 H 0.0845719215 -0.2904408219 1.0372016410 0.1041707902 + QMMM SCC-DFTB: 5 2 1 1 H 0.9744495193 0.2738752451 -0.3781261931 0.1041888187 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177297575948840 + QMMM SCC-DFTB: 2 -3.177297575949379 -0.000000000000539 0.000000028770979 2 2 H 0.10418 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.454267041583 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.465661958868 + QMMM SCC-DFTB: Total Energy (eV) = -87.919929000450 + QMMM SCC-DFTB: SCF Energy (eV) = -18.191037167850 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177297575949 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.053864827595 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231162403545 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668542343545 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.50350812779499 KCal/mol, -1755.20267800669421 KJ/mol +QMMM: +QMMM: Electronic energy = -86.45426704 eV ( -1993.72185225 KCal/mol) +QMMM: Repulsive energy = -1.46566196 eV ( -33.79963043 KCal/mol) +QMMM: Total energy = -87.91992900 eV ( -2027.52148268 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -0.08389606940974 -0.11995651422258 -0.11648189816041 +QMMM: Atm 2: 0.02409298945252 -0.01208920057537 0.01919866286834 +QMMM: Atm 3: 0.04593742903092 0.10270854098333 0.09298669811655 +QMMM: Atm 4: -0.02000477088421 -0.00089063282067 0.01917739144805 +QMMM: Atm 5: 0.03387042191143 0.03022780663044 -0.01488085456804 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C 0.0000038176 -0.0000741005 -0.0000915615 -0.4167784558 + QMMM SCC-DFTB: 2 2 1 1 H -0.6690925757 0.8440618436 -0.0841048900 0.1041805336 + QMMM SCC-DFTB: 3 2 1 1 H -0.3899329958 -0.8274219846 -0.5748810036 0.1042383039 + QMMM SCC-DFTB: 4 2 1 1 H 0.0845719140 -0.2904408194 1.0372015916 0.1041707818 + QMMM SCC-DFTB: 5 2 1 1 H 0.9744494919 0.2738752371 -0.3781261851 0.1041888366 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177297609890104 + QMMM SCC-DFTB: 2 -3.177297609902009 -0.000000000011905 0.000000031528976 2 2 H 0.10418 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.454267965434 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.465661033211 + QMMM SCC-DFTB: Total Energy (eV) = -87.919928998644 + QMMM SCC-DFTB: SCF Energy (eV) = -18.191037166044 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177297609902 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.053864793576 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231162403478 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668542343478 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.50350808614820 KCal/mol, -1755.20267783244412 KJ/mol +QMMM: +QMMM: Electronic energy = -86.45426797 eV ( -1993.72187355 KCal/mol) +QMMM: Repulsive energy = -1.46566103 eV ( -33.79960909 KCal/mol) +QMMM: Total energy = -87.91992900 eV ( -2027.52148264 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: -0.08396699091083 -0.11991097989157 -0.11648255229622 +QMMM: Atm 2: 0.02414617070286 -0.01215050708276 0.01920612150528 +QMMM: Atm 3: 0.04595307066413 0.10272477147955 0.09300363203994 +QMMM: Atm 4: -0.02000388964462 -0.00088812436557 0.01915299001483 +QMMM: Atm 5: 0.03387164178397 0.03022483954725 -0.01488018434134 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C 0.0000028335 -0.0000024337 0.0000027987 -0.4167784825 + QMMM SCC-DFTB: 2 2 1 1 H -0.6691668036 0.8441000307 -0.0841661042 0.1041805735 + QMMM SCC-DFTB: 3 2 1 1 H -0.3899499108 -0.8274546196 -0.5750132435 0.1042383013 + QMMM SCC-DFTB: 4 2 1 1 H 0.0846969405 -0.2904312731 1.0372413187 0.1041707840 + QMMM SCC-DFTB: 5 2 1 1 H 0.9744164720 0.2737884277 -0.3780667942 0.1041888237 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177269698695105 + QMMM SCC-DFTB: 2 -3.177269688959342 0.000000009735763 0.000046807800887 3 3 H 0.10418 + QMMM SCC-DFTB: 3 -3.177269657215860 0.000000031743483 0.000005855871898 1 1 C -0.41675 + QMMM SCC-DFTB: 4 -3.177269641375190 0.000000015840670 0.000000000735283 3 3 H 0.10419 + QMMM SCC-DFTB: 5 -3.177269641376874 -0.000000000001684 0.000000000023997 2 2 H 0.10419 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 5 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.453506941865 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.466423047235 + QMMM SCC-DFTB: Total Energy (eV) = -87.919929989100 + QMMM SCC-DFTB: SCF Energy (eV) = -18.191038156500 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177269641377 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.053892798502 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231162439879 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668542379879 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.50353092704279 KCal/mol, -1755.20277339874701 KJ/mol +QMMM: +QMMM: Electronic energy = -86.45350694 eV ( -1993.70432359 KCal/mol) +QMMM: Repulsive energy = -1.46642305 eV ( -33.81718189 KCal/mol) +QMMM: Total energy = -87.91992999 eV ( -2027.52150548 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: 0.00197580770225 -0.00035980687995 0.00070646556414 +QMMM: Atm 2: 0.00046647101156 -0.00106870093684 -0.00079556384126 +QMMM: Atm 3: -0.00072529720144 0.00096065618636 -0.00077488088056 +QMMM: Atm 4: -0.00020413609271 0.00017694635464 0.00105468965912 +QMMM: Atm 5: -0.00151284761905 0.00029090519209 -0.00019071050406 + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 2 6 C 0.0000028335 -0.0000024337 0.0000027987 -0.4167535319 + QMMM SCC-DFTB: 2 2 1 1 H -0.6691668036 0.8441000307 -0.0841661042 0.1041874493 + QMMM SCC-DFTB: 3 2 1 1 H -0.3899499108 -0.8274546196 -0.5750132435 0.1041881140 + QMMM SCC-DFTB: 4 2 1 1 H 0.0846969405 -0.2904312731 1.0372413187 0.1041892284 + QMMM SCC-DFTB: 5 2 1 1 H 0.9744164720 0.2737884277 -0.3780667942 0.1041887402 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-08 + QMMM SCC-DFTB: Charge: 5.0E-06 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -3.177269641376872 + QMMM SCC-DFTB: 2 -3.177269641376872 -0.000000000000000 0.000000000005430 2 2 H 0.10419 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 2 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -69.728891832600 + QMMM SCC-DFTB: Electronic Energy (eV) = -86.453506941865 + QMMM SCC-DFTB: Repulsive Energy (eV) = -1.466423047235 + QMMM SCC-DFTB: Total Energy (eV) = -87.919929989100 + QMMM SCC-DFTB: SCF Energy (eV) = -18.191038156500 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -2.562620060000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -3.177269641377 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = -0.053892798502 + QMMM SCC-DFTB: Total Energy (a.u.) = -3.231162439879 + QMMM SCC-DFTB: SCF Energy (a.u.) = -0.668542379879 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -419.50353092704194 KCal/mol, -1755.20277339874360 KJ/mol +QMMM: +QMMM: Electronic energy = -86.45350694 eV ( -1993.70432359 KCal/mol) +QMMM: Repulsive energy = -1.46642305 eV ( -33.81718189 KCal/mol) +QMMM: Total energy = -87.91992999 eV ( -2027.52150548 KCal/mol) +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: 0.00197580855841 -0.00035980761466 0.00070646591546 +QMMM: Atm 2: 0.00046647069005 -0.00106870058785 -0.00079556392153 +QMMM: Atm 3: -0.00072529733534 0.00096065631988 -0.00077488092885 +QMMM: Atm 4: -0.00020413624517 0.00017694651691 0.00105468945196 +QMMM: Atm 5: -0.00151284786736 0.00029090528194 -0.00019071051969 + ... geometry converged ! + + Final MO eigenvalues (au): + -0.5724 -0.3317 -0.3317 -0.3317 0.3784 0.3784 0.3784 0.6704 + + + Heat of formation = -419.50353093 kcal/mol ( -18.19103816 eV) + + Total SCF energy = -2027.52150548 kcal/mol ( -87.91992999 eV) + Electronic energy = -1993.70432359 kcal/mol ( -86.45350694 eV) + Core-core repulsion = -33.81718189 kcal/mol ( -1.46642305 eV) + + Atomic Charges for Step 1 : + Atom Element Mulliken Charge + 1 C -0.417 + 2 H 0.104 + 3 H 0.104 + 4 H 0.104 + 5 H 0.104 + Total Mulliken Charge = 0.000 + + X Y Z TOTAL + QM DIPOLE -0.000 0.000 -0.000 0.000 + + Final Structure + + QMMM: QM Region Cartesian Coordinates (*=link atom) + QMMM: QM_NO. MM_NO. ATOM X Y Z + QMMM: 1 1 C 0.0000 -0.0000 0.0000 + QMMM: 2 2 H -0.6692 0.8441 -0.0842 + QMMM: 3 3 H -0.3899 -0.8275 -0.5750 + QMMM: 4 4 H 0.0847 -0.2904 1.0372 + QMMM: 5 5 H 0.9744 0.2738 -0.3781 +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: 0.00197580855841 -0.00035980761466 0.00070646591546 +QMMM: Atm 2: 0.00046647069005 -0.00106870058785 -0.00079556392153 +QMMM: Atm 3: -0.00072529733534 0.00096065631988 -0.00077488092885 +QMMM: Atm 4: -0.00020413624517 0.00017694651691 0.00105468945196 +QMMM: Atm 5: -0.00151284786736 0.00029090528194 -0.00019071051969 + + --------- Calculation Completed ---------- + diff --git a/tests/test_amber_sqm.py b/tests/test_amber_sqm.py index 705e7ba9e..c8f762ba8 100644 --- a/tests/test_amber_sqm.py +++ b/tests/test_amber_sqm.py @@ -39,6 +39,22 @@ def tearDown(self) : if os.path.exists('tmp.sqm.forces'): shutil.rmtree('tmp.sqm.forces') + +class TestAmberSqmOutOpt(unittest.TestCase, CompLabeledSys, IsNoPBC): + def setUp(self) : + self.system_1 = dpdata.LabeledSystem('amber/sqm_opt.out', fmt = 'sqm/out') + self.system_1.to('deepmd/npy','tmp.sqm.opt') + self.system_2 = dpdata.LabeledSystem('tmp.sqm.opt', fmt = 'deepmd/npy') + self.places = 5 + self.e_places = 4 + self.f_places = 6 + self.v_places = 6 + + def tearDown(self) : + if os.path.exists('tmp.sqm.opt'): + shutil.rmtree('tmp.sqm.opt') + + @unittest.skipIf(skip_bond_order_system, "dpdata does not have BondOrderSystem. One may install rdkit to fix.") class TestAmberSqmIn(unittest.TestCase): def setUp(self):