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Steve Plimpton
2022-05-19 17:29:33 -06:00
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@ -0,0 +1,165 @@
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ITEM: ATOMS id x y z q fx fy fz
1 0.13513 -0.05627 0.09445000000000001 -0.8476 -1.074376566237102 7.775620147251701 32.74789761345844
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ITEM: ATOMS id x y z q fx fy fz
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2 0.8676775431393703 0.3662403256616637 -0.4718465920554844 0.4238 7.248596416342879 2.273259361466344 -11.07280694285822
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*****************************************************
* *
* PWDFT PSPW Calculation *
* *
* [ (Grassmann/Stiefel manifold implementation) ] *
* [ C++ implementation ] *
* *
* version #7.00 02/27/21 *
* *
* This code was developed by Eric J. Bylaska, *
* Abhishek Bagusetty, David H. Bross, ... *
* *
*****************************************************
>>> job started at Thu May 12 15:16:05 2022 <<<
psp_library: /home/sjplimp/lammps/git/lib/nwchem/PWDFT/Nwpw/libraryps
initializing nwpw_APC object
----------------------------
nga = 3 ngs = 9
Gc = 2.50000
APC gamma: 0 0.60000
APC gamma: 1 0.90000
APC gamma: 2 1.35000
APC u: 1 -0.02818
APC u: 2 -0.02183
APC u: 3 -0.04499
- self-consistent
reading formatted psp filename: ./O.vpp
reading formatted psp filename: ./H.vpp
input psi exists, reading from file: ./water-dimer.nw.movecs
============== summary of input ==================
input psi filename: ./water-dimer.nw.movecs
number of processors used: 8
processor grid : 8 x1
parallel mapping : 2d-hcurve
parallel mapping : balanced
options:
boundary conditions = periodic
electron spin = restricted
exchange-correlation = PBE96 (White and Bird) parameterization
elements involved in the cluster:
1: O valence charge : 6.0 lmax=2
comment : Parameterized (Chem.Phys.Lett., vol 322, page 447) Hamman psp
pseudopotential type : 0
highest angular component : 2
local potential used : 2
number of non-local projections : 4
cutoff = 0.700 0.700 0.700
2: H valence charge : 1.0 lmax=1
comment : Parameterized (Chem.Phys.Lett., vol 322, page 447) Hamman psp
pseudopotential type : 0
highest angular component : 1
local potential used : 1
number of non-local projections : 1
cutoff = 0.800 0.800
total charge: 0.000
atom composition:
O : 1 H : 2
initial ion positions (au):
1 O ( -0.00388 0.94060 5.30618 ) - atomic mass = 15.995
2 H ( -1.30565 1.65230 5.69814 ) - atomic mass = 1.008
3 H ( 0.52792 0.44858 4.18530 ) - atomic mass = 1.008
G.C. ( -0.26054 1.01383 5.06321 )
C.O.M. ( -0.04697 0.95289 5.26538 )
number of electrons: spin up= 4 ( 4 per task) down= 4 ( 4 per task)
supercell:
volume = 6748.33
lattice: a1=< 18.897 0.000 0.000 >
a2=< 0.000 18.897 0.000 >
a3=< 0.000 0.000 18.897 >
reciprocal: b1=< 0.332 0.000 0.000 >
b2=< 0.000 0.332 0.000 >
b3=< 0.000 0.000 0.332 >
lattice: a= 18.897 b= 18.897 c= 18.897
alpha= 90.000 beta= 90.000 gamma= 90.000
density cutoff= 100.000 fft= 90 x 90 x 90 ( 161227 waves 20153 per task)
wavefnc cutoff= 50.000 fft= 90 x 90 x 90 ( 56901 waves 7117 per task)
ewald parameters:
energy cutoff= 100.000 fft= 90 x 90 x 90 ( 161227 waves 20154 per task)
Ewald summation: cut radius= 6.015 and 1
Mandelung Wigner-Seitz= 1.76011888 (alpha= 2.83729748 rs=11.72292445)
technical parameters:
time step= 5.80 ficticious mass= 400000.00
tolerance= 1.000e-07 (energy) 1.000e-07 (density) 1.000e-04 (ion)
max iterations = 1000 ( 10 inner 100 outer)
minimizer = Grassmann conjugate gradient
============ Grassmann conjugate gradient iteration ============
>>> iteration started at Thu May 12 15:16:06 2022 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
10 -1.709044170181e+01 -9.440962e-08 1.468669e-17
*** tolerance ok. iteration terminated
>>> iteration ended at Thu May 12 15:16:13 2022 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 4.00000 down= 4.00000 (real space)
total energy : -1.7090441702e+01 ( -5.69681e+00 /ion)
total orbital energy: -4.4955483659e+00 ( -1.12389e+00 /electron)
hartree energy : 1.7961170991e+01 ( 4.49029e+00 /electron)
exc-corr energy : -4.4672372387e+00 ( -1.11681e+00 /electron)
ion-ion energy : 3.9861853815e+00 ( 1.32873e+00 /ion)
APC energy : -5.9166523032e-03 ( -1.97222e-03 /ion)
kinetic (planewave) : 1.3575166724e+01 ( 3.39379e+00 /electron)
V_local (planewave) : -4.6453534302e+01 ( -1.16134e+01 /electron)
V_nl (planewave) : -1.7461190799e+00 ( -4.36530e-01 /electron)
V_Coul (planewave) : 3.5922341982e+01 ( 8.98059e+00 /electron)
V_xc (planewave) : -5.7934036896e+00 ( -1.44835e+00 /electron)
K.S. V_APC energy : -5.9842474836e-02 ( -1.99475e-02 /ion)
Viral Coefficient : -1.3311597167e+00
orbital energy:
-2.8567573e-01 ( -7.774eV)
-3.1475928e-01 ( -8.565eV)
-6.4696668e-01 ( -17.605eV)
-1.0003725e+00 ( -27.222eV)
Ion Forces (au):
1 O ( -0.05636 0.12677 0.47582 )
2 H ( -0.15080 0.07727 0.02084 )
3 H ( 0.20660 -0.20381 -0.49586 )
*************************************************************
** **
** PSPW Atomic Point Charge (APC) Analysis **
** **
** Point charge analysis based on paper by P.E. Blochl **
** (J. Chem. Phys. vol 103, page 7422, 1995) **
** **
*************************************************************
nwpw_APC object
---------------
nga = 3 ngs = 9
Gc = 2.50000
APC gamma: 0 0.60000
APC gamma: 1 0.90000
APC gamma: 2 1.35000
- self-consistent
APC Potential:
-0.028176332 -0.021828211 -0.044988033
APC Point Charges:
-0.983228472 0.458254390 0.524974082
charge analysis on each atom
----------------------------
no atom Qelc Qion Qtotal
----- ---- ------- ------- -------
1 O -6.983 6.000 -0.983
2 H -0.542 1.000 0.458
3 H -0.475 1.000 0.525
Total Q -8.000 8.000 0.000
gaussian coefficients of model density
--------------------------------------
no atom g=0.000 g=0.600 g=0.900 g=1.350
----- ---- ------- ------- ------- -------
1 O 6.000 -1.261 -2.114 -3.608
2 H 1.000 -0.922 1.088 -0.707
3 H 1.000 -1.038 1.167 -0.604
output psi to filename: ./water-dimer.nw.movecs
-----------------
cputime in seconds
prologue : 6.70000e-01
main loop : 6.49000e+00
epilogue : 1.10000e-01
total : 7.27000e+00
cputime/step: 2.31786e-01 ( 28 evaluations, 9 linesearches)
Time spent doing total step percent
total time 6.156918e+03 2.198899e+02 100.00%
total FFT time 3.227409e+03 1.152646e+02 52.42%
lagrange multipliers 5.440821e-02 1.943150e-03 0.00%
local potentials 4.878728e+01 1.742403e+00 0.79%
non-local potentials 1.024134e+02 3.657620e+00 1.66%
ffm_dgemm 2.806113e+01 1.002183e+00 0.46%
fmf_dgemm 9.861207e+01 3.521860e+00 1.60%
m_diagonalize 1.641637e-01 5.862991e-03 0.00%
mmm_multiply 6.580998e-02 2.350357e-03 0.00%
>>> job completed at Thu May 12 15:16:13 2022 <<<

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examples/nwchem/log.pwdft.water.dimer.step=1.0 Normal file
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@ -0,0 +1,219 @@
*****************************************************
* *
* PWDFT PSPW Calculation *
* *
* [ (Grassmann/Stiefel manifold implementation) ] *
* [ C++ implementation ] *
* *
* version #7.00 02/27/21 *
* *
* This code was developed by Eric J. Bylaska, *
* Abhishek Bagusetty, David H. Bross, ... *
* *
*****************************************************
>>> job started at Thu May 12 11:58:41 2022 <<<
psp_library: /home/sjplimp/lammps/git/lib/nwchem/PWDFT/Nwpw/libraryps
initializing nwpw_APC object
----------------------------
nga = 3 ngs = 9
Gc = 2.50000
APC gamma: 0 0.60000
APC gamma: 1 0.90000
APC gamma: 2 1.35000
APC u: 1 -0.02793
APC u: 2 -0.02191
APC u: 3 -0.04698
- self-consistent
reading formatted psp filename: ./O.vpp
reading formatted psp filename: ./H.vpp
input psi exists, reading from file: ./water-dimer.nw.movecs
============== summary of input ==================
input psi filename: ./water-dimer.nw.movecs
number of processors used: 8
processor grid : 8 x1
parallel mapping : 2d-hcurve
parallel mapping : balanced
options:
boundary conditions = periodic
electron spin = restricted
exchange-correlation = PBE96 (White and Bird) parameterization
elements involved in the cluster:
1: O valence charge : 6.0 lmax=2
comment : Parameterized (Chem.Phys.Lett., vol 322, page 447) Hamman psp
pseudopotential type : 0
highest angular component : 2
local potential used : 2
number of non-local projections : 4
cutoff = 0.700 0.700 0.700
2: H valence charge : 1.0 lmax=1
comment : Parameterized (Chem.Phys.Lett., vol 322, page 447) Hamman psp
pseudopotential type : 0
highest angular component : 1
local potential used : 1
number of non-local projections : 1
cutoff = 0.800 0.800
total charge: 0.000
atom composition:
O : 1 H : 2
initial ion positions (au):
1 O ( -0.01117 0.94608 5.31429 ) - atomic mass = 15.995
2 H ( -1.25842 1.62529 5.69093 ) - atomic mass = 1.008
3 H ( 0.59969 0.38947 4.07419 ) - atomic mass = 1.008
G.C. ( -0.22330 0.98695 5.02647 )
C.O.M. ( -0.04679 0.95294 5.26596 )
number of electrons: spin up= 4 ( 4 per task) down= 4 ( 4 per task)
supercell:
volume = 6748.33
lattice: a1=< 18.897 0.000 0.000 >
a2=< 0.000 18.897 0.000 >
a3=< 0.000 0.000 18.897 >
reciprocal: b1=< 0.332 0.000 0.000 >
b2=< 0.000 0.332 0.000 >
b3=< 0.000 0.000 0.332 >
lattice: a= 18.897 b= 18.897 c= 18.897
alpha= 90.000 beta= 90.000 gamma= 90.000
density cutoff= 100.000 fft= 90 x 90 x 90 ( 161227 waves 20153 per task)
wavefnc cutoff= 50.000 fft= 90 x 90 x 90 ( 56901 waves 7117 per task)
ewald parameters:
energy cutoff= 100.000 fft= 90 x 90 x 90 ( 161227 waves 20154 per task)
Ewald summation: cut radius= 6.015 and 1
Mandelung Wigner-Seitz= 1.76011888 (alpha= 2.83729748 rs=11.72292445)
technical parameters:
time step= 5.80 ficticious mass= 400000.00
tolerance= 1.000e-07 (energy) 1.000e-07 (density) 1.000e-04 (ion)
max iterations = 1000 ( 10 inner 100 outer)
minimizer = Grassmann conjugate gradient
============ Grassmann conjugate gradient iteration ============
>>> iteration started at Thu May 12 11:58:42 2022 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
10 -1.713577000794e+01 -4.591815e-04 5.628517e-14
20 -1.713650758172e+01 -1.808515e-05 3.740401e-14
30 -1.713653420240e+01 -8.346322e-07 5.434141e-15
40 -1.713653653723e+01 -9.258308e-08 4.724058e-16
*** tolerance ok. iteration terminated
>>> iteration ended at Thu May 12 11:59:10 2022 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 4.00000 down= 4.00000 (real space)
total energy : -1.7136536537e+01 ( -5.71218e+00 /ion)
total orbital energy: -4.4259619721e+00 ( -1.10649e+00 /electron)
hartree energy : 1.7765965957e+01 ( 4.44149e+00 /electron)
exc-corr energy : -4.4301498454e+00 ( -1.10754e+00 /electron)
ion-ion energy : 3.6785658332e+00 ( 1.22619e+00 /ion)
APC energy : -6.8890938229e-03 ( -2.29636e-03 /ion)
kinetic (planewave) : 1.3374096079e+01 ( 3.34352e+00 /electron)
V_local (planewave) : -4.5924717414e+01 ( -1.14812e+01 /electron)
V_nl (planewave) : -1.6619742191e+00 ( -4.15494e-01 /electron)
V_Coul (planewave) : 3.5531931914e+01 ( 8.88298e+00 /electron)
V_xc (planewave) : -5.7452983317e+00 ( -1.43632e+00 /electron)
K.S. V_APC energy : -6.8566165946e-02 ( -2.28554e-02 /ion)
Viral Coefficient : -1.3309354102e+00
orbital energy:
-2.8382851e-01 ( -7.723eV)
-3.1172375e-01 ( -8.483eV)
-6.3236398e-01 ( -17.208eV)
-9.8506475e-01 ( -26.805eV)
Ion Forces (au):
1 O ( 0.16012 -0.04303 0.16025 )
2 H ( -0.23409 0.12188 0.04418 )
3 H ( 0.07412 -0.07900 -0.20449 )
*************************************************************
** **
** PSPW Atomic Point Charge (APC) Analysis **
** **
** Point charge analysis based on paper by P.E. Blochl **
** (J. Chem. Phys. vol 103, page 7422, 1995) **
** **
*************************************************************
nwpw_APC object
---------------
nga = 3 ngs = 9
Gc = 2.50000
APC gamma: 0 0.60000
APC gamma: 1 0.90000
APC gamma: 2 1.35000
- self-consistent
APC Potential:
-0.027925866 -0.021908598 -0.046977988
APC Point Charges:
-0.970516556 0.462767804 0.507748752
charge analysis on each atom
----------------------------
no atom Qelc Qion Qtotal
----- ---- ------- ------- -------
1 O -6.971 6.000 -0.971
2 H -0.537 1.000 0.463
3 H -0.492 1.000 0.508
Total Q -8.000 8.000 0.000
gaussian coefficients of model density
--------------------------------------
no atom g=0.000 g=0.600 g=0.900 g=1.350
----- ---- ------- ------- ------- -------
1 O 6.000 -1.256 -2.061 -3.654
2 H 1.000 -0.995 1.184 -0.726
3 H 1.000 -0.956 1.105 -0.642
output psi to filename: ./water-dimer.nw.movecs
-----------------
cputime in seconds
prologue : 6.50000e-01
main loop : 2.82100e+01
epilogue : 1.10000e-01
total : 2.89700e+01
cputime/step: 2.29350e-01 ( 123 evaluations, 9 linesearches)
Time spent doing total step percent
total time 3.184996e+02 2.589428e+00 100.00%
total FFT time 1.872118e+02 1.522047e+00 58.78%
lagrange multipliers 5.308966e-02 4.316232e-04 0.02%
local potentials 2.312943e+00 1.880441e-02 0.73%
non-local potentials 5.446934e+00 4.428402e-02 1.71%
ffm_dgemm 1.615372e+00 1.313311e-02 0.51%
fmf_dgemm 5.699877e+00 4.634046e-02 1.79%
m_diagonalize 1.025786e-02 8.339727e-05 0.00%
mmm_multiply 4.933436e-03 4.010924e-05 0.00%
>>> job completed at Thu May 12 11:59:10 2022 <<<

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LAMMPS (4 May 2022)
# MM for water dimer
units real
atom_style full
bond_style harmonic
angle_style harmonic
read_data data.water.dimer
Reading data file ...
orthogonal box = (-5 -5 -5) to (5 5 5)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
group mm molecule 1
3 atoms in group mm
group qm molecule 2
3 atoms in group qm
# pair style must define stand-alone short-range Coulombics
pair_style lj/cut/coul/cut 6.0
pair_coeff 1 1 0.13506 3.166
pair_coeff 2 2 0.0 1.0
velocity all create 300.0 458732
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
compute 1 all pair/local dist
compute 2 all reduce max c_1
variable fxabs atom abs(fx)
variable fyabs atom abs(fy)
variable fzabs atom abs(fz)
variable qabs atom abs(q)
compute 3 all reduce max v_fxabs v_fyabs v_fzabs v_qabs
dump 1 all custom 1 dump.water.dimer.mm id x y z q fx fy fz
dump_modify 1 sort id format float "%20.16g"
timestep 0.1
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong pe etotal press c_2 c_3[*]
thermo 1
run 100
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/cut/coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) compute pair/local, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.814 | 7.814 | 7.814 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long PotEng TotEng Press c_2 c_3[1] c_3[2] c_3[3] c_3[4]
0 0 300 4.4712151 1.4460769 -8.6451874 -7.1991105 3.3067213 0 -3.8923892 0.57882592 3501.9716 3.6506239 29.132518 26.894893 39.12903 0.8476
1 0.000108574 285.13363 4.249646 1.4375279 -8.6406901 -7.2031621 3.5325983 0 -3.6705638 0.57908212 3614.6958 3.6464898 29.314431 30.404171 38.108216 0.8476
2 0.000216888 270.14782 4.0262967 1.4290421 -8.6397116 -7.2106695 3.7637147 0 -3.4469549 0.57934187 3709.3988 3.6425559 29.356146 33.782878 41.024451 0.8476
3 0.000317085 255.32078 3.8053137 1.4206323 -8.6422685 -7.2216361 3.9959226 0 -3.2257135 0.5796002 3785.896 3.6388405 31.590054 37.014455 44.820312 0.8476
4 0.000408338 240.92922 3.5908212 1.4123113 -8.6483639 -7.2360525 4.2250834 0 -3.0109691 0.57985214 3844.0886 3.6353606 34.007291 40.083016 48.357581 0.8476
5 0.000495879 227.24308 3.3868423 1.4040912 -8.6579872 -7.253896 4.4471465 0 -2.8067495 0.58009281 3883.9583 3.6321321 36.282114 42.973422 51.619538 0.8476
6 0.000595848 214.52029 3.1972211 1.3959835 -8.6711139 -7.2751304 4.6582269 0 -2.6169035 0.58031757 3905.5628 3.6291698 38.403224 45.671352 54.590895 0.8476
7 0.000690563 203.00175 3.0255483 1.3879994 -8.6877054 -7.299706 4.8546798 0 -2.4450263 0.58052204 3909.0296 3.6264872 40.360011 48.163379 57.25787 0.8476
8 0.000780788 192.90672 2.8750914 1.3801493 -8.7077084 -7.3275592 5.03317 0 -2.2943892 0.58070222 3894.5514 3.6240965 42.142609 50.437027 59.608252 0.8476
9 0.000869152 184.42845 2.748731 1.3724429 -8.7310548 -7.3586119 5.1907355 0 -2.1678764 0.58085457 3862.3805 3.6220086 43.741945 52.480839 61.631459 0.8476
10 0.000962443 177.73046 2.6489038 1.3648896 -8.7576613 -7.3927717 5.324844 0 -2.0679277 0.58097607 3812.8237 3.6202329 45.149781 54.284429 63.318585 0.8476
11 0.00105142 172.94325 2.577555 1.3574978 -8.7874291 -7.4299313 5.4334407 0 -1.9964907 0.58106428 3746.2374 3.6187774 46.358757 55.838538 64.662439 0.8476
12 0.001137597 170.16172 2.5360988 1.3502751 -8.8202436 -7.4699685 5.5149871 0 -1.9549814 0.58111741 3663.0237 3.6176486 47.362428 57.135076 65.657575 0.8476
13 0.001255333 169.44321 2.5253901 1.3432287 -8.8559744 -7.5127456 5.5684898 0 -1.9442558 0.5811343 3563.6262 3.6168515 48.155295 58.167168 66.300317 0.8476
14 0.001369762 170.80633 2.5457061 1.3363649 -8.8944745 -7.5581097 5.5935181 0 -1.9645915 0.58111454 3448.5266 3.6163895 48.73284 58.929186 66.588769 0.8476
15 0.001457514 174.23042 2.596739 1.329689 -8.9355811 -7.6058921 5.5902115 0 -2.0156806 0.58105836 3318.2421 3.6162647 49.091543 59.416783 66.522817 0.8476
16 0.001541406 179.65591 2.6776006 1.3232059 -8.9791148 -7.6559088 5.5592749 0 -2.0966339 0.58096674 3173.3232 3.6164774 49.228909 59.626917 66.104129 0.8476
17 0.001624611 186.98526 2.7868377 1.3169195 -9.0248798 -7.7079604 5.501964 0 -2.2059963 0.58084132 3014.3518 3.6170265 49.143481 59.557868 65.336134 0.8476
18 0.001713422 196.08479 2.9224575 1.3108328 -9.0726648 -7.761832 5.4200588 0 -2.3417731 0.5806844 2841.9408 3.6179093 48.834849 59.209249 64.224005 0.8476
19 0.001798708 206.78712 3.0819656 1.3049483 -9.1222424 -7.817294 5.3158273 0 -2.5014667 0.58049889 2656.7333 3.6191218 48.303661 58.582019 62.774623 0.8476
20 0.001880692 218.89428 3.2624113 1.2992676 -9.1733703 -7.8741026 5.1919796 0 -2.682123 0.58028826 2459.4027 3.6206582 47.55162 57.678475 60.996542 0.8476
21 0.00196951 232.18142 3.4604436 1.2937914 -9.2257915 -7.9320001 5.051613 0 -2.8803871 0.58005648 2250.6534 3.6225641 46.581483 56.502249 58.899935 0.8476
22 0.002063019 246.4011 3.6723744 1.2885196 -9.2792356 -7.990716 4.8981495 0 -3.0925665 0.57980792 2031.2217 3.6260815 45.397051 55.058297 56.496544 0.8476
23 0.002146555 261.28792 3.8942483 1.2834517 -9.3334195 -8.0499678 4.7352669 0 -3.314701 0.5795473 1801.8772 3.6296949 44.003153 53.352876 53.799614 0.8476
24 0.002251198 276.56359 4.1219177 1.278586 -9.3880487 -8.1094627 4.5668246 0 -3.5426381 0.57927957 1563.4241 3.633394 42.405634 51.393519 50.823822 0.8476
25 0.002351296 291.94228 4.3511224 1.2739202 -9.4428184 -8.1688982 4.3967857 0 -3.7721125 0.57900986 1316.7028 3.6371685 40.611323 49.189004 47.585204 0.8476
26 0.002436139 307.13602 4.5775707 1.2694515 -9.4974158 -8.2279643 4.229137 0 -3.9988273 0.57874331 1062.5915 3.6410075 38.628012 46.749316 44.101067 0.8476
27 0.002517578 321.86029 4.797022 1.2651761 -9.551521 -8.2863449 4.067808 0 -4.2185369 0.57848506 802.00755 3.6448998 36.464415 44.085601 41.406795 0.8476
28 0.002604486 335.83949 5.0053686 1.2610896 -9.6048094 -8.3437198 3.9165913 0 -4.4271285 0.57824005 535.9089 3.6488343 34.130138 41.210115 44.10716 0.8476
29 0.0026898 348.81219 5.1987145 1.2571871 -9.6569537 -8.3997666 3.7790651 0 -4.6207014 0.57801304 265.29457 3.6527995 31.635628 38.136171 46.657468 0.8476
30 0.002773029 360.53631 5.3734513 1.2534629 -9.7076257 -8.4541628 3.6585199 0 -4.7956429 0.5778084 -8.794746 3.656784 28.992133 34.878073 49.045375 0.8476
31 0.002855462 370.79371 5.526328 1.2499107 -9.7564992 -8.5065884 3.5578905 0 -4.9486979 0.57763011 -285.27697 3.6607762 27.62239 32.182847 51.259321 0.8476
32 0.002943797 379.3945 5.6545146 1.2465238 -9.8032516 -8.5567279 3.4796949 0 -5.077033 0.57748165 -563.02946 3.6647645 26.563572 29.797288 53.288577 0.8476
33 0.003030293 386.18075 5.7556573 1.2432946 -9.8475672 -8.6042726 3.4259812 0 -5.1782914 0.57736592 -840.89063 3.6687378 25.375082 27.259723 55.123309 0.8476
34 0.003113837 391.02961 5.827925 1.2402154 -9.8891387 -8.6489233 3.3982836 0 -5.2506397 0.57728522 -1117.6623 3.6726846 24.062447 24.582642 56.754618 0.8476
35 0.003205052 393.85572 5.8700454 1.2372778 -9.9276704 -8.6903926 3.3975883 0 -5.2928043 0.57724115 -1392.1132 3.6765939 22.631838 21.779274 58.174591 0.8476
36 0.00333772 394.61297 5.8813315 1.234473 -9.9628799 -8.7284069 3.42431 0 -5.3040969 0.57723463 -1662.9826 3.6804549 22.1841 18.863529 59.376335 0.8476
37 0.003459581 393.29544 5.861695 1.2317918 -9.994501 -8.7627093 3.4782801 0 -5.2844292 0.57726585 -1928.9861 3.6846426 23.596149 15.849925 60.354015 0.8476
38 0.003546305 389.93764 5.8116501 1.2292246 -10.022286 -8.7930611 3.5587453 0 -5.2343159 0.57733426 -2188.8208 3.6896572 24.897159 16.33096 61.102879 0.8476
39 0.003647059 384.61386 5.7323043 1.2267616 -10.046006 -8.8192445 3.6643788 0 -5.1548657 0.57743861 -2441.1731 3.6946813 26.080685 17.116789 61.619281 0.8476
40 0.003734658 377.43688 5.6253383 1.2243927 -10.065456 -8.8410636 3.7933023 0 -5.0477613 0.57757694 -2684.7253 3.699693 27.140845 17.813611 61.900699 0.8476
41 0.003822249 368.55583 5.4929746 1.2221076 -10.080455 -8.8583471 3.943119 0 -4.915228 0.57774662 -2918.1652 3.7046705 28.072353 18.41852 61.945746 0.8476
42 0.003907418 358.15337 5.3379359 1.2198956 -10.090844 -8.8709487 4.1109572 0 -4.7599915 0.57794442 -3140.1942 3.7095927 28.870544 18.929064 61.754172 0.8476
43 0.004000453 346.44225 5.1633927 1.2177461 -10.096495 -8.8787492 4.2935231 0 -4.5852261 0.57816655 -3349.5379 3.7144383 29.531397 19.34326 61.326869 0.8476
44 0.004088816 333.66121 4.9729034 1.2156484 -10.097305 -8.8816569 4.4871623 0 -4.3944946 0.57840875 -3544.9561 3.719187 30.051559 20.34722 60.66586 0.8476
45 0.004183228 320.07043 4.7703457 1.2135917 -10.0932 -8.8796086 4.6879293 0 -4.1916794 0.57866635 -3725.253 3.7238187 30.428358 24.214592 59.774286 0.8476
46 0.004278607 305.94652 4.5598423 1.2115652 -10.084135 -8.8725699 4.891662 0 -3.980908 0.57893437 -3889.2889 3.7283141 30.65982 27.968201 58.656393 0.8476
47 0.004367758 291.57719 4.3456811 1.2095584 -10.070094 -8.8605354 5.0940619 0 -3.7664735 0.57920762 -4035.9902 3.7326547 30.744677 31.589809 57.317501 0.8476
48 0.004459797 277.25567 4.1322324 1.2075606 -10.051089 -8.8435284 5.2907768 0 -3.5527516 0.5794808 -4164.3608 3.7368229 30.682376 35.061795 55.76398 0.8476
49 0.004546987 263.27502 3.9238641 1.2055614 -10.027162 -8.8216009 5.4774855 0 -3.3441155 0.57974859 -4273.4924 3.7408018 30.794569 38.367231 54.003214 0.8476
50 0.004638731 249.92244 3.7248566 1.2035507 -9.9983835 -8.7948328 5.6499819 0 -3.1448508 0.58000576 -4362.5748 3.7445759 33.382629 41.489976 56.003406 0.8476
51 0.004727684 237.47368 3.5393196 1.2015187 -9.9648493 -8.7633307 5.8042583 0 -2.9590724 0.58024727 -4430.9054 3.7481304 35.814306 44.414749 58.436055 0.8476
52 0.004814581 226.18762 3.3711116 1.1994557 -9.9266829 -8.7272273 5.9365841 0 -2.7906432 0.58046839 -4477.8981 3.7514521 38.077898 47.127208 60.568812 0.8476
53 0.004900573 216.30119 3.2237638 1.1973525 -9.8840323 -8.6866798 6.0435808 0 -2.643099 0.58066475 -4503.0912 3.7545288 40.162494 49.614021 62.390703 0.8476
54 0.004992228 208.02471 3.1004107 1.1952004 -9.837069 -8.6418686 6.1222903 0 -2.5195782 0.58083247 -4506.1544 3.7573496 42.058026 51.862932 63.892309 0.8476
55 0.005088966 201.5377 3.003728 1.1929912 -9.7859863 -8.5929952 6.1702353 0 -2.4227599 0.58096819 -4486.8947 3.7599052 43.755322 53.862822 65.065803 0.8476
56 0.005184769 196.98532 2.9358791 1.1907168 -9.7309979 -8.540281 6.1854711 0 -2.35481 0.58106918 -4445.2607 3.7621874 45.246153 55.603766 65.90499 0.8476
57 0.005323812 194.4754 2.8984711 1.1883703 -9.6723353 -8.4839651 6.1666273 0 -2.3173378 0.58113336 -4381.3461 3.7641898 46.523274 57.077084 66.405331 0.8476
58 0.005416242 194.07624 2.8925221 1.1859447 -9.6102467 -8.424302 6.1129393 0 -2.3113627 0.58115939 -4295.3914 3.7659072 47.580464 58.27538 66.563967 0.8476
59 0.005503175 195.81517 2.9184391 1.1834341 -9.5449945 -8.3615604 6.0242679 0 -2.3372925 0.58114662 -4187.7839 3.7673361 48.412555 59.192585 66.379724 0.8476
60 0.005588728 199.67782 2.9760082 1.180833 -9.4768532 -8.2960202 5.9011071 0 -2.394913 0.58109517 -4059.057 3.7684744 49.015463 59.823986 65.853118 0.8476
61 0.005680657 205.6083 3.0643965 1.1781367 -9.4061076 -8.2279709 5.7445803 0 -2.4833906 0.58100592 -3909.8873 3.7693219 49.386211 60.16625 64.986348 0.8476
62 0.005767373 213.51013 3.1821657 1.1753411 -9.3330507 -8.1577096 5.5564244 0 -2.6012852 0.58088047 -3741.0902 3.7698794 49.522944 60.217443 63.78328 0.8476
63 0.005851809 223.24791 3.3272981 1.1724428 -9.2579816 -8.0855388 5.3389619 0 -2.746577 0.58072112 -3553.6142 3.7701498 49.424941 59.97704 62.249421 0.8476
64 0.005940043 234.64984 3.497233 1.1694392 -9.1812036 -8.0117644 5.0950622 0 -2.9167022 0.58053084 -3348.5343 3.7701372 49.092622 59.44593 60.391891 0.8476
65 0.006024298 247.51088 3.6889146 1.1663285 -9.1030224 -7.9366939 4.8280925 0 -3.1086014 0.5803132 -3127.0428 3.7698473 48.52755 58.626416 58.219379 0.8476
66 0.006106867 261.59658 3.8988485 1.1631094 -9.0237441 -7.8606347 4.5418585 0 -3.3187762 0.58007231 -2890.4406 3.7692873 47.732427 57.5222 55.742095 0.8476
67 0.00619933 276.64748 4.1231679 1.1597815 -8.9436736 -7.7838922 4.240537 0 -3.5433552 0.57981273 -2640.1254 3.7684659 46.711078 56.138371 52.971715 0.8476
68 0.006289684 292.38403 4.3577063 1.1563451 -8.8631133 -7.7067682 3.9286014 0 -3.7781668 0.57953941 -2377.5811 3.767393 45.468445 54.48138 49.921318 0.8476
69 0.00637265 308.51186 4.5980763 1.1528013 -8.7823612 -7.6295599 3.6107411 0 -4.0188187 0.57925757 -2104.3643 3.7660801 44.010558 52.559013 46.605313 0.8476
70 0.00647451 324.7274 4.8397535 1.1491519 -8.7017097 -7.5525578 3.2917769 0 -4.260781 0.57897259 -1822.0918 3.7645399 42.344513 50.380351 43.039366 0.8476
71 0.006611144 340.72367 5.0781626 1.1453993 -8.6214447 -7.4760454 2.9765727 0 -4.4994727 0.57868996 -1532.4266 3.7627862 40.478437 47.955732 39.240314 0.8476
72 0.006766842 356.1961 5.3087646 1.1415467 -8.541844 -7.4002973 2.6699478 0 -4.7303495 0.57841511 -1237.0642 3.7608341 38.421457 45.296699 35.908965 0.8476
73 0.006910635 370.84845 5.527144 1.1375978 -8.4631768 -7.325579 2.3765883 0 -4.9489906 0.57815335 -937.71844 3.7586997 36.183651 42.415949 33.149638 0.8476
74 0.007063711 384.39844 5.7290937 1.1335571 -8.3857026 -7.2521455 2.1009615 0 -5.151184 0.57790975 -636.10731 3.7564001 33.776008 39.327269 30.227725 0.8476
75 0.007234606 396.58322 5.9106962 1.1294296 -8.3096707 -7.180241 1.8472339 0 -5.3330071 0.57768903 -333.93957 3.7539531 31.210375 36.045477 28.27021 0.8476
76 0.007388818 407.16441 6.0683988 1.1252209 -8.2353195 -7.1100985 1.6191952 0 -5.4909033 0.57749551 -32.90115 3.7513776 28.499399 32.586346 30.335839 0.8476
77 0.007545872 415.93279 6.1990832 1.1209372 -8.162876 -7.0419388 1.4201886 0 -5.6217502 0.57733299 265.35747 3.748693 25.80438 28.96653 32.25767 0.8476
78 0.007698043 422.71234 6.3001259 1.1165849 -8.0925557 -6.9759708 1.2530496 0 -5.7229212 0.57720466 559.23333 3.7459193 24.546107 25.20349 34.027204 0.8476
79 0.007859655 427.36367 6.3694496 1.1121711 -8.0245619 -6.9123908 1.1200543 0 -5.7923365 0.5771131 847.18211 3.7454697 23.16537 21.315405 35.636681 0.8476
80 0.008014214 429.78684 6.4055647 1.1077033 -7.959086 -6.8513827 1.0228782 0 -5.8285045 0.57706019 1127.7283 3.7458911 21.669308 17.886615 37.079109 0.8476
81 0.008163682 429.92332 6.4075988 1.1031893 -7.8963069 -6.7931177 0.9625659 0 -5.8305518 0.57704704 1399.4742 3.7464014 21.504773 14.667654 38.348302 0.8476
82 0.008332187 427.75725 6.3753156 1.0986371 -7.8363914 -6.7377544 0.93951286 0 -5.7982415 0.57707404 1661.1079 3.7470107 22.938641 13.924922 39.438903 0.8476
83 0.008497655 423.31584 6.3091205 1.094055 -7.779494 -6.685439 0.95345929 0 -5.7319797 0.5771408 1911.4098 3.7477287 24.258263 14.650513 40.346408 0.8476
84 0.008646946 416.66895 6.210055 1.0894517 -7.7257567 -6.6363051 1.0034963 0 -5.6328088 0.57724617 2149.258 3.7485645 25.45701 15.296903 41.067187 0.8476
85 0.008740288 407.92792 6.0797782 1.0848358 -7.6753098 -6.590474 1.0880841 0 -5.5023899 0.57738827 2373.6322 3.7495268 26.528835 15.861142 41.598497 0.8476
86 0.008862209 397.2435 5.920537 1.0802161 -7.6282712 -6.548055 1.2050825 0 -5.3429725 0.57756449 2583.6169 3.7506236 27.468299 16.340706 41.938491 0.8476
87 0.008965034 384.8031 5.7351247 1.0756016 -7.5847469 -6.5091453 1.3517921 0 -5.1573531 0.57777159 2778.4024 3.7518624 28.270601 16.733505 42.086229 0.8476
88 0.009051301 370.82733 5.5268292 1.0710011 -7.5448312 -6.4738301 1.5250066 0 -4.9488235 0.57800572 2957.285 3.7532501 28.931602 17.037894 42.041676 0.8476
89 0.009137301 355.56589 5.2993718 1.0664236 -7.5086067 -6.4421831 1.7210738 0 -4.7211093 0.57826252 3119.6665 3.754793 29.447848 20.109526 45.39414 0.8476
90 0.009241849 339.29283 5.0568374 1.0618777 -7.4761442 -6.4142665 1.9359662 0 -4.4783003 0.57853717 3265.052 3.7564965 29.816582 24.058838 49.598524 0.8476
91 0.009332198 322.30151 4.8035979 1.0573723 -7.4475032 -6.3901309 2.1653575 0 -4.2247734 0.5788245 3393.0469 3.7583655 30.035766 27.892627 53.610309 0.8476
92 0.009417236 304.89898 4.5442297 1.0529158 -7.4227313 -6.3698156 2.404705 0 -3.9651106 0.57911912 3503.353 3.7604039 30.104088 31.591932 57.411853 0.8476
93 0.009506343 287.40021 4.2834272 1.0485165 -7.401865 -6.3533486 2.6493368 0 -3.7040118 0.57941545 3595.7643 3.762615 30.020967 35.138407 60.98654 0.8476
94 0.009592085 270.12217 4.0259145 1.0441825 -7.384929 -6.3407465 2.89454 0 -3.4462066 0.57970789 3670.1611 3.7650013 29.786564 38.514416 64.318849 0.8476
95 0.009677533 253.37777 3.7763551 1.0399217 -7.3719365 -6.3320149 3.1356507 0 -3.1963642 0.5799909 3726.5054 3.7675644 30.257703 41.703118 67.394414 0.8476
96 0.009761808 237.46995 3.5392641 1.0357414 -7.362889 -6.3271475 3.3681425 0 -2.959005 0.58025909 3764.8341 3.7703052 32.611486 44.688549 70.200084 0.8476
97 0.00985092 222.6859 3.3189219 1.031649 -7.3577759 -6.3261269 3.5877124 0 -2.7384145 0.58050737 3785.2532 3.7732238 34.78904 47.455705 72.723966 0.8476
98 0.009937676 209.29162 3.1192929 1.0276512 -7.3565751 -6.3289238 3.790362 0 -2.5385619 0.58073101 3787.9318 3.7763192 36.779137 49.990618 74.955474 0.8476
99 0.01002271 197.52682 2.9439497 1.0237544 -7.3592517 -6.3354973 3.9724734 0 -2.3630239 0.58092573 3773.096 3.7795899 38.571494 52.280425 76.885367 0.8476
100 0.010107748 187.60034 2.7960049 1.0199646 -7.3657588 -6.3457942 4.1308771 0 -2.2149171 0.58108781 3741.023 3.7830333 40.156828 54.313433 78.505775 0.8476
Loop time of 0.0101317 on 1 procs for 100 steps with 6 atoms
Performance: 85.277 ns/day, 0.281 hours/ns, 9869.971 timesteps/s
87.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00016668 | 0.00016668 | 0.00016668 | 0.0 | 1.65
Bond | 0.00014462 | 0.00014462 | 0.00014462 | 0.0 | 1.43
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00014401 | 0.00014401 | 0.00014401 | 0.0 | 1.42
Output | 0.0095231 | 0.0095231 | 0.0095231 | 0.0 | 93.99
Modify | 5.49e-05 | 5.49e-05 | 5.49e-05 | 0.0 | 0.54
Other | | 9.839e-05 | | | 0.97
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 138 ave 138 max 138 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 11 ave 11 max 11 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 11
Ave neighs/atom = 1.8333333
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (4 May 2022)
# MM for water dimer
units real
atom_style full
bond_style harmonic
angle_style harmonic
read_data data.water.dimer
Reading data file ...
orthogonal box = (-5 -5 -5) to (5 5 5)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
group mm molecule 1
3 atoms in group mm
group qm molecule 2
3 atoms in group qm
# pair style must define stand-alone short-range Coulombics
pair_style lj/cut/coul/cut 6.0
pair_coeff 1 1 0.13506 3.166
pair_coeff 2 2 0.0 1.0
velocity all create 300.0 458732
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
compute 1 all pair/local dist
compute 2 all reduce max c_1
variable fxabs atom abs(fx)
variable fyabs atom abs(fy)
variable fzabs atom abs(fz)
variable qabs atom abs(q)
compute 3 all reduce max v_fxabs v_fyabs v_fzabs v_qabs
dump 1 all custom 1 dump.water.dimer.mm id x y z q fx fy fz
dump_modify 1 sort id format float "%20.16g"
timestep 1.0
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong pe etotal press c_2 c_3[*]
thermo 1
run 10
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/cut/coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) compute pair/local, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.814 | 7.814 | 7.814 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long PotEng TotEng Press c_2 c_3[1] c_3[2] c_3[3] c_3[4]
0 0 300 4.4712151 1.4460769 -8.6451874 -7.1991105 3.3067213 0 -3.8923892 0.57882592 3501.9716 3.6506239 29.132518 26.894893 39.12903 0.8476
1 9.0821e-05 173.62441 2.5877069 1.3627751 -8.7586622 -7.395887 5.6398836 0 -1.7560034 0.83170352 3873.6649 3.6174036 47.207927 56.887589 66.270405 0.8476
2 0.000184033 205.00005 3.0553311 1.2966054 -9.1890483 -7.8924429 5.6109802 0 -2.2814627 0.77386841 2473.2868 3.6189736 49.892973 60.637964 64.087423 0.8476
3 0.000280209 345.25808 5.1457438 1.2520821 -9.7382996 -8.4862175 3.8346933 0 -4.6515242 0.4942196 -91.739394 3.6572584 29.616414 35.651548 51.229515 0.8476
4 0.000378667 362.92645 5.409074 1.2253056 -10.089434 -8.8641281 3.9207917 0 -4.9433364 0.46573762 -2843.4092 3.7021652 27.859069 18.30959 62.335363 0.8476
5 0.000474038 236.16047 3.5197476 1.2063245 -9.9863303 -8.7800058 6.0013284 0 -2.7786774 0.74107014 -4493.6796 3.748768 37.005758 45.993677 60.476842 0.8476
6 0.000574805 193.80377 2.8884612 1.1837524 -9.4198967 -8.2361443 6.1975906 0 -2.0385537 0.84990749 -4019.2838 3.7713021 51.868439 63.346091 68.596527 0.8476
7 0.000665971 324.35592 4.8342169 1.1502259 -8.6211435 -7.4709176 3.2339214 0 -4.2369962 0.59722074 -1558.4031 3.7633516 42.077838 50.013491 41.435238 0.8476
8 0.000753783 415.75227 6.1963928 1.1059493 -7.8912735 -6.7853242 0.99561798 0 -5.7897063 0.40668652 1490.3717 3.7429867 22.4649 13.94175 39.268564 0.8476
9 0.000839444 308.74121 4.6014946 1.0579776 -7.4537941 -6.3958165 2.4023073 0 -3.9935092 0.60798533 3505.5339 3.7551919 30.183856 31.816344 57.223547 0.8476
10 0.000945335 170.83878 2.5461898 1.0158762 -7.4078206 -6.3919444 4.7159988 0 -1.6759456 0.87024423 3699.5818 3.7846626 45.070133 60.452465 83.454556 0.8476
Loop time of 0.000970251 on 1 procs for 10 steps with 6 atoms
Performance: 890.491 ns/day, 0.027 hours/ns, 10306.611 timesteps/s
89.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6409e-05 | 1.6409e-05 | 1.6409e-05 | 0.0 | 1.69
Bond | 1.7408e-05 | 1.7408e-05 | 1.7408e-05 | 0.0 | 1.79
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3548e-05 | 1.3548e-05 | 1.3548e-05 | 0.0 | 1.40
Output | 0.00090469 | 0.00090469 | 0.00090469 | 0.0 | 93.24
Modify | 5.592e-06 | 5.592e-06 | 5.592e-06 | 0.0 | 0.58
Other | | 1.261e-05 | | | 1.30
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 138 ave 138 max 138 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 11 ave 11 max 11 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 11
Ave neighs/atom = 1.8333333
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (4 May 2022)
# QMMM with NWChem for water dimer
units real
atom_style full
bond_style harmonic
angle_style harmonic
read_data data.water.dimer
Reading data file ...
orthogonal box = (-5 -5 -5) to (5 5 5)
2 by 2 by 2 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.008 seconds
group mm molecule 1
3 atoms in group mm
group qm molecule 2
3 atoms in group qm
# remove bonds/angles in QM water molecule
delete_bonds qm multi remove special
System init for delete_bonds ...
Deleting bonds ...
2 total bonds, 2 turned on, 0 turned off
1 total angles, 1 turned on, 0 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# pair style must define stand-alone short-range Coulombics
pair_style hybrid/overlay lj/cut 6.0 coul/cut 6.0
pair_coeff 1 1 lj/cut 0.13506 3.166
pair_coeff 2 2 lj/cut 0.0 1.0
pair_coeff * * coul/cut
velocity all create 300.0 458732
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 qm nwchem template-water.nw water-dimer.nw log.pwdft.water-dimer O H
fix_modify 2 energy yes
compute 1 all pair/local dist
compute 2 all reduce max c_1
variable fxabs atom abs(fx)
variable fyabs atom abs(fy)
variable fzabs atom abs(fz)
variable qabs atom abs(q)
compute 3 all reduce max v_fxabs v_fyabs v_fzabs v_qabs
dump 1 all custom 1 dump.water.dimer.qmmm id x y z q fx fy fz
dump_modify 1 sort id format float "%20.16g"
timestep 0.1
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong f_2 pe etotal press c_2 c_3[*]
thermo 1
run 100
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 3 3 3
3 neighbor lists, perpetual/occasional/extra = 2 1 0
(1) pair lj/cut, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(3) compute pair/local, occasional, copy from (2)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.608 | 8.391 | 8.875 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press c_2 c_3[1] c_3[2] c_3[3] c_3[4]
0 0 300 4.4712151 1.4460769 -156.41522 -154.96914 1.5216554 0 -10694.103 -10847.551 -10843.079 -1340.3569 3.6506239 65.178593 52.412068 222.20969 0.8476
1 7.9635392 279.1936 4.1611154 1.4378132 -156.07977 -154.64196 1.74291 0 -10694.371 -10847.27 -10843.109 -1205.0695 3.6464367 64.928115 51.883891 222.63383 0.8476
2 17.078844 271.867 4.0519194 1.4301758 -155.93775 -154.50757 1.9798148 0 -10694.501 -10847.028 -10842.977 -1074.2697 3.642344 64.427572 51.313909 222.47363 0.8476
3 26.133342 278.19509 4.1462335 1.4231658 -155.97731 -154.55414 2.22745 0 -10694.522 -10846.849 -10842.703 -948.04686 3.6383646 63.750928 50.620854 222.01948 0.8476
4 35.011228 298.26363 4.4453362 1.4167839 -156.22381 -154.80703 2.4806908 0 -10694.411 -10846.737 -10842.292 -827.34584 3.6345172 62.894316 49.820862 221.10162 0.8476
5 46.471117 332.08118 4.9493546 1.4110296 -156.78816 -155.37713 2.7343085 0 -10694.085 -10846.728 -10841.779 -715.06525 3.6308201 61.859426 48.92674 220.9264 0.8476
6 59.396825 379.59473 5.6574989 1.405904 -157.60698 -156.20108 2.9830734 0 -10693.571 -10846.789 -10841.131 -610.10907 3.6272914 60.654822 47.924487 219.10495 0.8476
7 72.486458 440.6387 6.5673014 1.4014044 -158.56073 -157.15932 3.2218577 0 -10692.939 -10846.877 -10840.309 -510.12526 3.6239485 59.250638 47.89597 217.81619 0.8476
8 86.305839 514.90849 7.674222 1.3975292 -159.79848 -158.40095 3.4457374 0 -10692.07 -10847.025 -10839.351 -418.94692 3.6208081 57.650782 50.155722 215.77533 0.8476
9 101.22114 601.99417 8.9721514 1.394275 -161.37431 -159.98004 3.6500885 0 -10690.904 -10847.234 -10838.262 -338.26249 3.6178864 55.900553 52.185203 212.91874 0.8476
10 116.2172 701.29997 10.45221 1.3916367 -163.0733 -161.68166 3.8306772 0 -10689.572 -10847.423 -10836.971 -263.69518 3.6151991 53.89421 53.972978 210.02036 0.8476
11 131.32403 811.98677 12.101892 1.3896089 -165.0332 -163.6436 3.9837448 0 -10687.946 -10847.606 -10835.504 -199.05426 3.6127609 51.65995 55.51073 206.46063 0.8476
12 147.10768 933.0438 13.906132 1.3881845 -167.27195 -165.88377 4.1060803 0 -10685.983 -10847.76 -10833.854 -145.48743 3.610586 49.223569 56.790642 202.54886 0.8476
13 162.9575 1063.2079 15.846104 1.3873553 -169.81309 -168.42574 4.1950837 0 -10683.626 -10847.857 -10832.011 -104.40643 3.6086877 48.215617 57.806155 197.72471 0.8476
14 178.81479 1200.8925 17.898162 1.3871111 -172.67378 -171.28667 4.2488165 0 -10680.822 -10847.86 -10829.962 -77.262191 3.6070788 48.77664 58.551924 191.99683 0.8476
15 194.70921 1344.1851 20.033802 1.3874392 -175.87525 -174.48782 4.2660398 0 -10677.505 -10847.727 -10827.693 -65.787806 3.6057708 49.11919 59.023911 185.18753 0.8476
16 210.54171 1490.7704 22.218516 1.3883245 -179.43994 -178.05162 4.2462383 0 -10673.604 -10847.409 -10825.191 -71.986058 3.6047748 49.241041 59.219386 177.08061 0.8476
17 226.33039 1637.8639 24.410806 1.3897484 -183.39572 -182.00598 4.1896305 0 -10669.034 -10846.851 -10822.44 -98.273137 3.6041009 49.141005 59.136969 167.39749 0.8476
18 242.06042 1782.1304 26.56096 1.3916882 -187.76796 -186.37628 4.0971639 0 -10663.705 -10845.985 -10819.424 -147.35289 3.6037583 48.818943 58.776598 155.76952 0.8476
19 258.00548 1919.6018 28.609842 1.3941165 -192.58607 -191.19196 3.9704965 0 -10657.516 -10844.738 -10816.128 -222.42286 3.6037551 48.275769 58.139569 141.77074 0.8476
20 275.35265 2045.863 30.491645 1.3969999 -197.88269 -196.48569 3.8119643 0 -10650.359 -10843.032 -10812.541 -327.02978 3.6040989 47.513375 57.228513 126.9171 0.8476
21 292.73884 2155.5236 32.126032 1.4003018 -203.67404 -202.27373 3.6245353 0 -10642.115 -10840.764 -10808.638 -464.97891 3.6047956 46.534921 56.047385 106.59274 0.8476
22 310.16175 2242.2039 33.41792 1.4039726 -209.98708 -208.58311 3.4117515 0 -10632.669 -10837.84 -10804.422 -640.96628 3.6058506 45.344415 54.601468 82.056851 0.8476
23 327.46334 2299.208 34.267512 1.4079518 -216.83411 -215.42616 3.1776593 0 -10621.915 -10834.163 -10799.896 -859.53826 3.6072682 43.946948 52.89733 52.630632 0.8476
24 344.8631 2319.6379 34.572 1.4121662 -224.21449 -222.80232 2.9267307 0 -10609.769 -10829.645 -10795.073 -1125.053 3.6090515 42.348625 50.942806 43.509548 0.8476
25 362.21893 2297.0314 34.235071 1.4165282 -232.10781 -230.69129 2.6637754 0 -10596.192 -10824.22 -10789.985 -1441.0888 3.6112028 43.768937 48.746962 54.124553 0.8476
26 379.50446 2226.343 33.181528 1.4209344 -240.46944 -239.0485 2.3938473 0 -10581.214 -10817.868 -10784.687 -1809.6724 3.6137226 55.730219 56.26722 101.30713 0.8476
27 395.57396 2104.976 31.372668 1.425265 -249.19273 -247.76747 2.1221456 0 -10564.986 -10810.632 -10779.259 -2229.713 3.6166108 69.232431 73.121566 154.60725 0.8476
28 411.83487 1934.9262 28.838238 1.4293802 -258.18366 -256.75428 1.8539135 0 -10547.781 -10802.681 -10773.843 -2697.2456 3.6198658 83.915478 91.252147 212.11925 0.8476
29 427.94825 1724.1741 25.697177 1.4331317 -267.24705 -265.81391 1.5943358 0 -10530.069 -10794.288 -10768.591 -3201.8785 3.6234846 99.465881 110.21119 272.2629 0.8476
30 443.97701 1487.0138 22.162528 1.4363634 -276.15597 -274.7196 1.3484386 0 -10512.501 -10785.873 -10763.71 -3728.1549 3.6274626 115.24433 129.13136 332.10381 0.8476
31 459.99058 1244.1016 18.542152 1.4389185 -284.63634 -283.19742 1.1209909 0 -10495.907 -10777.983 -10759.441 -4255.1643 3.6317941 130.37974 146.88911 387.91422 0.85122875
32 475.2309 1020.5477 15.210295 1.4406492 -292.38614 -290.94549 0.91641266 0 -10481.225 -10771.254 -10756.043 -4758.2791 3.6364718 143.82706 162.21057 435.57619 0.85860515
33 490.70704 842.45939 12.556057 1.4414268 -299.10632 -297.66489 0.73868922 0 -10469.397 -10766.323 -10753.767 -5212.2138 3.6414866 154.44721 173.74254 470.80473 0.86512891
34 504.70323 732.17448 10.912365 1.4411542 -304.29501 -302.85386 0.59129405 0 -10461.394 -10763.657 -10752.744 -5589.5656 3.6468283 161.31844 180.52039 490.80714 0.8702794
35 517.97102 703.81011 10.489621 1.4397743 -308.13708 -306.69731 0.477122 0 -10457.485 -10763.706 -10753.216 -5884.1768 3.6524849 163.47558 181.56002 492.73096 0.8744856
36 531.11756 760.03073 11.327536 1.4372731 -310.57613 -309.13886 0.39843348 0 -10457.827 -10766.568 -10755.24 -6092.1284 3.6584431 160.54776 176.62307 476.23104 0.8777428
37 544.61935 891.25176 13.283261 1.433683 -311.57382 -310.14014 0.35681116 0 -10462.237 -10772.02 -10758.737 -6218.2107 3.6646876 152.68771 166.11314 443.04619 0.87998416
38 559.05607 1077.968 16.066089 1.4290793 -311.13199 -309.70291 0.35312963 0 -10470.212 -10779.562 -10763.496 -6274.8468 3.6712019 140.48936 150.94127 396.48594 0.8811141
39 574.10271 1295.1047 19.302306 1.4235712 -309.42593 -308.00236 0.38753854 0 -10480.962 -10788.577 -10769.274 -6282.1799 3.6779681 124.83354 132.28969 340.56233 0.88123026
40 589.09934 1516.8523 22.607242 1.4172912 -306.71972 -305.30243 0.45945957 0 -10493.576 -10798.419 -10775.812 -6262.853 3.6849668 106.77903 111.45546 279.42956 0.88052774
41 604.88421 1720.7855 25.646674 1.4103831 -303.30009 -301.88971 0.56759719 0 -10507.177 -10808.5 -10782.853 -6237.6983 3.6921772 96.475116 89.745768 217.0457 0.8792327
42 620.85225 1890.3414 28.173744 1.4029913 -299.40019 -297.9972 0.70996312 0 -10521.042 -10818.329 -10790.155 -6222.3155 3.6995773 99.144511 70.014579 156.51237 0.87751226
43 637.10877 2015.6457 30.041284 1.3952552 -295.22892 -293.83367 0.88391378 0 -10534.602 -10827.551 -10797.51 -6227.1877 3.7071437 100.76473 70.562027 100.17025 0.87552632
44 653.08943 2093.078 31.19534 1.3873019 -290.94963 -289.56233 1.0862002 0 -10547.471 -10835.947 -10804.752 -6257.497 3.7148517 101.24445 70.328176 49.415938 0.87340323
45 669.23915 2123.8969 31.654666 1.3792434 -286.68805 -285.3088 1.3130295 0 -10559.414 -10843.409 -10811.755 -6314.2519 3.7226755 100.52478 69.286035 45.668211 0.87124886
46 685.19705 2112.6399 31.486891 1.3711754 -282.53593 -281.16475 1.5601365 0 -10570.314 -10849.919 -10818.432 -6395.4678 3.7305881 99.328609 70.830069 48.909823 0.8691468
47 700.95723 2065.6535 30.786604 1.3631768 -278.55781 -277.19463 1.8228644 0 -10580.14 -10855.512 -10824.726 -6497.3293 3.7385614 109.54698 81.422448 77.94289 0.86716204
48 717.23951 1989.9498 29.658312 1.3553119 -274.79068 -273.43537 2.0962529 0 -10588.921 -10860.26 -10830.602 -6614.9691 3.7465665 117.07385 89.501173 103.68602 0.8653337
49 733.03677 1892.4346 28.20494 1.3476311 -271.25475 -269.90712 2.3751324 0 -10596.717 -10864.249 -10836.044 -6743.2471 3.7545737 122.12317 95.318561 124.77471 0.86368557
50 749.0192 1779.4528 26.521053 1.3401737 -267.95951 -266.61934 2.6542218 0 -10603.602 -10867.567 -10841.046 -6877.2052 3.7625527 124.95672 99.155658 141.87452 0.86223115
51 764.95048 1656.5819 24.68978 1.3329692 -264.90585 -263.57288 2.9282288 0 -10609.656 -10870.301 -10845.611 -7012.263 3.7704731 125.86312 101.30091 155.60795 0.86097351
52 780.77673 1528.5886 22.782161 1.3260394 -262.09191 -260.76587 3.1919501 0 -10614.958 -10872.532 -10849.749 -7144.3881 3.7783039 125.13271 102.03075 166.52439 0.85991242
53 796.6081 1399.4809 20.857934 1.3193996 -259.51286 -258.19346 3.4403709 0 -10619.577 -10874.33 -10853.472 -7270.062 3.7860148 123.04881 101.6034 175.09813 0.85904267
54 812.65306 1272.6064 18.966989 1.3130602 -257.16482 -255.85176 3.6687594 0 -10623.576 -10875.759 -10856.792 -7386.3076 3.7935754 119.87389 100.24935 181.72412 0.85835951
55 828.70467 1150.7626 17.151023 1.3070275 -255.04377 -253.73674 3.8727579 0 -10627.011 -10876.875 -10859.724 -7490.5962 3.8009564 115.8464 98.171764 188.07046 0.85785667
56 843.84601 1036.2751 15.444697 1.3013049 -253.14077 -251.83947 4.0484647 0 -10629.934 -10877.725 -10862.28 -7580.689 3.808129 111.20629 95.583152 193.70694 0.85751789
57 858.87222 931.14889 13.87789 1.2958942 -251.4695 -250.17361 4.1925097 0 -10632.373 -10878.354 -10864.476 -7655.1676 3.8150656 106.04465 92.526617 198.2226 0.85736384
58 873.88225 837.12557 12.476562 1.2907944 -250.02253 -248.73173 4.3021181 0 -10634.368 -10878.798 -10866.322 -7712.4004 3.82174 100.5832 89.193613 201.81155 0.8573781
59 888.93394 755.67941 11.262684 1.2860035 -248.80491 -247.5189 4.3751639 0 -10635.947 -10879.09 -10867.828 -7751.3151 3.8281275 94.9416 85.841238 204.60376 0.85756429
60 904.09531 688.08468 10.255249 1.2815185 -247.82053 -246.53901 4.4102108 0 -10637.129 -10879.258 -10869.002 -7771.0436 3.8342051 96.315965 87.779469 206.69536 0.8579228
61 918.009 635.41522 9.4702604 1.2773358 -247.19208 -245.91475 4.40654 0 -10637.882 -10879.39 -10869.92 -7773.6648 3.8399515 98.744368 89.446547 208.27648 0.85866449
62 931.98076 598.60951 8.9217062 1.273451 -246.69429 -245.42084 4.3641647 0 -10638.318 -10879.375 -10870.453 -7753.4928 3.8453474 100.85001 90.809159 209.16215 0.85937978
63 945.62659 578.45867 8.621377 1.2698603 -246.4367 -245.16684 4.2838301 0 -10638.399 -10879.282 -10870.661 -7712.6898 3.8503751 102.64344 91.89519 209.47574 0.86025227
64 959.31981 575.55449 8.578093 1.2665595 -246.44284 -245.17628 4.1670005 0 -10638.117 -10879.126 -10870.548 -7651.6814 3.8550194 104.13391 92.71503 209.2432 0.86131194
65 972.8238 590.2997 8.7978564 1.2635443 -246.72839 -245.46484 4.0158316 0 -10637.463 -10878.912 -10870.114 -7570.9345 3.8592668 105.31961 93.267808 208.46207 0.86257322
66 986.56015 622.89619 9.2836762 1.2608102 -247.31065 -246.04984 3.8331308 0 -10636.421 -10878.638 -10869.354 -7471.1779 3.863106 106.19065 93.545016 207.11202 0.8640516
67 999.86608 673.32374 10.035251 1.2583521 -248.20988 -246.95153 3.6223041 0 -10634.969 -10878.298 -10868.263 -7353.4435 3.8665277 106.72937 93.530626 205.1543 0.8657656
68 1014.0071 741.32087 11.048683 1.2561648 -249.45984 -248.20368 3.3872926 0 -10633.048 -10877.864 -10866.815 -7219.3161 3.8695246 106.93395 93.219282 202.57369 0.86775085
69 1028.4415 826.3417 12.315838 1.2542415 -251.07559 -249.82135 3.132498 0 -10630.664 -10877.353 -10865.037 -7070.2205 3.8720916 106.72214 92.543786 199.22005 0.87001927
70 1043.6944 927.50667 13.823606 1.2525754 -253.11792 -251.86535 2.8626995 0 -10627.717 -10876.719 -10862.896 -6908.922 3.8742253 106.08637 91.488315 195.04256 0.8726447
71 1058.734 1043.5374 15.552934 1.2511579 -255.56753 -254.31637 2.5829638 0 -10624.197 -10875.931 -10860.378 -6736.688 3.8759245 104.90781 89.944522 189.76857 0.87556881
72 1073.7507 1172.6691 17.477519 1.2499794 -258.4777 -257.22772 2.298549 0 -10620.01 -10874.939 -10857.462 -6556.831 3.8771893 103.10661 87.836026 183.21855 0.87884845
73 1088.7494 1312.5696 19.562604 1.2490288 -261.88764 -260.63861 2.0148053 0 -10615.065 -10873.689 -10854.126 -6372.7736 3.878022 100.558 85.046678 175.11752 0.88251321
74 1104.8293 1460.2565 21.763736 1.2482919 -265.84323 -264.59494 1.7370738 0 -10609.255 -10872.113 -10850.349 -6188.5736 3.8784261 97.121531 81.449419 165.18221 0.88659941
75 1121.0167 1611.8828 24.023582 1.247752 -270.38188 -269.13413 1.4705854 0 -10602.46 -10870.124 -10846.1 -6008.7148 3.8784071 92.556977 76.813113 152.83011 0.89112269
76 1137.1103 1762.5655 26.269365 1.2473872 -275.55354 -274.30615 1.2203616 0 -10594.54 -10867.626 -10841.356 -5838.6968 3.8779715 90.384772 70.923091 137.57808 0.89611643
77 1152.9983 1906.3234 28.41194 1.2471697 -281.40624 -280.15907 0.99111937 0 -10585.336 -10864.504 -10836.092 -5684.7397 3.8771276 93.025527 63.500478 118.77999 0.90160675
78 1168.9924 2035.9426 30.34379 1.2470642 -287.98344 -286.73637 0.78718145 0 -10574.682 -10860.631 -10830.287 -5553.8063 3.8758846 95.400108 60.435713 95.681996 0.90761054
79 1185.1206 2142.9841 31.939142 1.2470267 -295.32188 -294.07485 0.61239432 0 -10562.404 -10855.866 -10823.927 -5453.5424 3.8742532 97.505618 61.539466 67.464181 0.9141359
80 1201.0566 2217.9978 33.05715 1.2470021 -303.44501 -302.19801 0.47005494 0 -10548.341 -10850.068 -10817.011 -5391.9722 3.8741579 99.333218 62.464688 41.932314 0.92117689
81 1216.7261 2251.0684 33.550037 1.2469225 -312.35465 -311.10773 0.36284788 0 -10532.366 -10843.111 -10809.561 -5376.9308 3.8751842 100.86789 63.203625 54.051571 0.9287087
82 1232.6607 2232.8159 33.278 1.2467057 -322.00783 -320.76113 0.29279394 0 -10514.437 -10834.905 -10801.627 -5414.8469 3.8758879 102.08374 73.851092 103.00759 0.9366648
83 1248.7032 2155.9604 32.132543 1.246254 -332.31447 -331.06822 0.26121117 0 -10494.629 -10825.436 -10793.303 -5509.6177 3.8762714 126.62887 97.566268 159.04319 0.94494781
84 1264.5344 2017.4519 30.068205 1.2454541 -343.1221 -341.87664 0.26868919 0 -10473.205 -10814.813 -10784.745 -5660.8038 3.876338 155.35646 123.97958 221.42746 0.95342357
85 1280.5484 1820.8834 27.138537 1.2441795 -354.19785 -352.95367 0.31507711 0 -10450.676 -10803.314 -10776.176 -5861.5683 3.8760923 186.15438 152.36407 288.43751 0.96191146
86 1296.5803 1578.6098 23.527679 1.2422939 -365.22196 -363.97967 0.39948537 0 -10427.847 -10791.427 -10767.9 -6097.0791 3.8755402 217.65338 181.4766 357.19116 0.97018787
87 1311.7423 1312.6414 19.563674 1.2396586 -375.7836 -374.54394 0.52030148 0 -10405.834 -10779.858 -10760.294 -6343.7995 3.8746894 247.89056 209.61609 423.98975 0.97798259
88 1326.7781 1053.5275 15.701827 1.236141 -385.42523 -384.18909 0.67521937 0 -10385.985 -10769.499 -10753.797 -6571.2576 3.8735493 274.44676 234.46238 483.2272 0.98502605
89 1341.8473 836.35996 12.465151 1.2316279 -393.65565 -392.42403 0.86128191 0 -10369.752 -10761.315 -10748.85 -6745.0607 3.8721312 294.69969 253.74767 530.07201 0.99103027
90 1356.0045 694.2772 10.347542 1.226036 -399.9031 -398.67706 1.0749357 0 -10358.556 -10756.158 -10745.811 -6830.2443 3.8704491 306.66316 265.56814 559.82289 0.99558422
91 1370.3127 651.34531 9.7076832 1.2193228 -404.07892 -402.8596 1.3120976 0 -10353.19 -10754.737 -10745.029 -6809.0025 3.8685194 307.96838 268.06491 569.40825 0.99880989
92 1384.8197 716.48198 10.678483 1.2114928 -405.96895 -404.75745 1.568231 0 -10354.088 -10757.278 -10746.599 -6670.9128 3.8663614 298.04559 260.64063 557.29708 1.0005428
93 1399.7586 880.84268 13.128124 1.2026 -405.7461 -404.5435 1.8384312 0 -10360.915 -10763.62 -10750.492 -6426.4345 3.8639975 276.91675 243.34984 524.06935 1.0009681
94 1414.7873 1119.8631 16.690495 1.1927448 -403.47609 -402.28335 2.1175187 0 -10372.933 -10773.099 -10756.409 -6094.2201 3.8614533 246.6651 218.13268 473.75775 0.99999914
95 1430.8978 1399.1305 20.852711 1.1820635 -399.6557 -398.47364 2.4001373 0 -10388.792 -10784.866 -10764.013 -5709.4225 3.8587581 209.27161 186.82634 410.83336 0.99799645
96 1447.0059 1681.5637 25.06211 1.170717 -394.75039 -393.57968 2.6808565 0 -10407.042 -10797.941 -10772.879 -5308.2406 3.855945 166.39347 151.141 339.64393 0.99524025
97 1462.828 1934.042 28.82506 1.15888 -389.23707 -388.07819 2.954276 0 -10426.271 -10811.395 -10782.57 -4924.3852 3.8530512 120.70224 113.46879 265.43619 0.99202725
98 1478.6255 2131.8683 31.773472 1.1467284 -383.5404 -382.39367 3.2151297 0 -10445.288 -10824.467 -10792.693 -4584.5886 3.8501178 74.159255 75.632628 192.31812 0.98863238
99 1494.5018 2260.3492 33.688358 1.1344307 -378.00308 -376.86865 3.4583878 0 -10463.2 -10836.61 -10802.922 -4306.8537 3.8471903 37.781342 50.321111 123.23383 0.98528822
100 1510.189 2314.1789 34.490639 1.122141 -372.87682 -371.75468 3.6793544 0 -10479.42 -10847.495 -10813.004 -4100.6713 3.8443182 39.43071 52.360106 72.144107 0.98217642
Loop time of 1510.19 on 8 procs for 100 steps with 6 atoms
Performance: 0.001 ns/day, 41949.696 hours/ns, 0.066 timesteps/s
99.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00055038 | 0.00070352 | 0.00088492 | 0.0 | 0.00
Bond | 0.00015422 | 0.00022842 | 0.000407 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0023861 | 0.0025905 | 0.002668 | 0.2 | 0.00
Output | 0.014997 | 0.015145 | 0.015297 | 0.1 | 0.00
Modify | 1510.2 | 1510.2 | 1510.2 | 0.0 |100.00
Other | | 0.0005933 | | | 0.00
Nlocal: 0.75 ave 2 max 0 min
Histogram: 3 0 0 0 0 4 0 0 0 1
Nghost: 43.25 ave 48 max 38 min
Histogram: 1 2 1 0 0 0 0 0 0 4
Neighs: 1.75 ave 3 max 0 min
Histogram: 3 0 0 0 0 0 1 0 0 4
Total # of neighbors = 14
Ave neighs/atom = 2.3333333
Ave special neighs/atom = 1
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:25:56

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examples/nwchem/log.water.dimer.qmmm.step=1.0 Normal file
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LAMMPS (4 May 2022)
# QMMM with NWChem for water dimer
units real
atom_style full
bond_style harmonic
angle_style harmonic
read_data data.water.dimer
Reading data file ...
orthogonal box = (-5 -5 -5) to (5 5 5)
2 by 2 by 2 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.008 seconds
group mm molecule 1
3 atoms in group mm
group qm molecule 2
3 atoms in group qm
# remove bonds/angles in QM water molecule
delete_bonds qm multi remove special
System init for delete_bonds ...
Deleting bonds ...
2 total bonds, 2 turned on, 0 turned off
1 total angles, 1 turned on, 0 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# pair style must define stand-alone short-range Coulombics
pair_style hybrid/overlay lj/cut 6.0 coul/cut 6.0
pair_coeff 1 1 lj/cut 0.13506 3.166
pair_coeff 2 2 lj/cut 0.0 1.0
pair_coeff * * coul/cut
velocity all create 300.0 458732
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 qm nwchem template-water.nw water-dimer.nw log.pwdft.water-dimer O H
fix_modify 2 energy yes
compute 1 all pair/local dist
compute 2 all reduce max c_1
variable fxabs atom abs(fx)
variable fyabs atom abs(fy)
variable fzabs atom abs(fz)
variable qabs atom abs(q)
compute 3 all reduce max v_fxabs v_fyabs v_fzabs v_qabs
dump 1 all custom 1 dump.water.dimer.qmmm id x y z q fx fy fz
dump_modify 1 sort id format float "%20.16g"
timestep 1.0
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong f_2 pe etotal press c_2 c_3[*]
thermo 1
run 10
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 3 3 3
3 neighbor lists, perpetual/occasional/extra = 2 1 0
(1) pair lj/cut, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(3) compute pair/local, occasional, copy from (2)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.608 | 8.391 | 8.875 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press c_2 c_3[1] c_3[2] c_3[3] c_3[4]
0 0 300 4.4712151 1.4460769 -156.41522 -154.96914 1.5216554 0 -10694.103 -10847.551 -10843.079 -1340.3569 3.6506239 65.178593 52.412068 222.20969 0.8476
1 22.715723 681.41106 10.155785 1.3902526 -162.9859 -161.59565 4.1525204 0 -10689.627 -10847.07 -10836.914 -182.89855 3.6120678 53.480757 56.561538 209.87713 0.8476
2 52.706709 1844.7745 27.494612 1.3967207 -199.02831 -197.63159 4.1843464 0 -10648.589 -10842.036 -10814.542 -396.38694 3.5999829 49.831379 60.160325 121.24755 0.8476
3 83.466947 798.98361 11.908092 1.4446268 -287.28082 -285.8362 1.4052139 0 -10483.806 -10768.237 -10756.329 -4437.7116 3.6251961 144.52194 165.39539 447.46935 0.8522356
4 107.62839 1199.8846 17.883141 1.3979159 -285.93825 -284.54034 0.52314438 0 -10543.094 -10827.111 -10809.228 -6122.5806 3.6871981 104.7406 74.603564 93.868472 0.86374008
5 136.61304 1035.1666 15.428175 1.3321872 -258.27431 -256.94212 3.106051 0 -10616.533 -10870.369 -10854.941 -7355.1014 3.770288 120.80841 99.457321 163.13492 0.85329214
6 163.96251 578.55841 8.6228637 1.2935848 -248.71519 -247.4216 4.8610652 0 -10632.542 -10875.103 -10866.48 -7990.0046 3.8432774 87.947868 80.489092 190.64995 0.85736994
7 189.61565 1169.2133 17.426013 1.2789846 -269.72482 -268.44584 2.8071856 0 -10599.543 -10865.182 -10847.756 -7053.7012 3.877965 82.28135 66.365452 134.06562 0.88559635
8 217.46091 874.74996 13.037317 1.2750847 -349.2097 -347.93462 0.33535001 0 -10452.504 -10800.104 -10787.066 -7098.5338 3.8708362 194.33729 159.46404 297.45568 0.95572863
9 243.07442 972.90915 14.500287 1.2039558 -380.07172 -378.86776 1.5743027 0 -10426.747 -10804.041 -10789.54 -5899.3431 3.8584754 171.62486 147.05796 303.88319 0.98487954
10 272.07801 955.04443 14.23403 1.0840146 -350.12961 -349.0456 4.4227883 0 -10541.358 -10885.981 -10871.746 -4337.6635 3.8290441 195.81841 129.79496 166.45654 0.97051656
Loop time of 272.078 on 8 procs for 10 steps with 6 atoms
Performance: 0.003 ns/day, 7557.723 hours/ns, 0.037 timesteps/s
99.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.164e-05 | 7.9711e-05 | 9.976e-05 | 0.0 | 0.00
Bond | 1.3004e-05 | 2.1651e-05 | 4.3958e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00024574 | 0.00028172 | 0.00030177 | 0.0 | 0.00
Output | 0.0015524 | 0.0015772 | 0.0016038 | 0.0 | 0.00
Modify | 272.08 | 272.08 | 272.08 | 0.0 |100.00
Other | | 7.495e-05 | | | 0.00
Nlocal: 0.75 ave 2 max 0 min
Histogram: 3 0 0 0 0 4 0 0 0 1
Nghost: 43.25 ave 48 max 38 min
Histogram: 1 2 1 0 0 0 0 0 0 4
Neighs: 1.75 ave 3 max 0 min
Histogram: 3 0 0 0 0 0 1 0 0 4
Total # of neighbors = 14
Ave neighs/atom = 2.3333333
Ave special neighs/atom = 1
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:05:18