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organize NWChem examples

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This commit is contained in:
Steve Plimpton
2023-02-08 16:06:45 -07:00
parent 2cd32d7e76
commit 618e766d5f
23 changed files with 7099 additions and 88 deletions
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28
examples/QUANTUM/LATTE/README
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@ -1,17 +1,17 @@
# Test runs of AIMD with LAMMPS and LATTE
# Test runs with coupling of LAMMPS and LATTE
Step 1: build LAMMPS
Step 2: download/build the MDI code coupling package
Step 3: download/build or install LATTE
Step 4: run the water AIMD problem for a few steps
Step 2: download/build MDI code coupling package
Step 3: download/build LATTE
Step 4: perform test runs in any of 3 modes
---------------------------------
---------------------------------
Step 1: build LAMMPS
The molecule package is needed. Copy the final LAMMPS executable into
the examples/QUANTUM/LATTE directory.
The MDI and molecule packags are needed. Copy the final LAMMPS
executable into the examples/QUANTUM/LATTE directory.
Traditional make:
@ -60,6 +60,14 @@ For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git
% rehash
(d) Check import of 3 Python modules which the script that wraps LATTE
will need:
% python
>>> import numpy as np
>>> from mpi4py import MPI
>>> import MDI_Library as mdi
---------------------------------
---------------------------------
@ -75,7 +83,7 @@ Step 3: download/build LATTE
% cd ~/latte/git
% mkdir build; cd build
% cmake -DBUILD_SHARED_LIBS=on ../cmake
% make
% make # should produce liblatte.so in build
(c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that
the liblatte.so file can be found:
@ -104,7 +112,7 @@ in.sucrose = AIMD of sucrose molecule
in.uo2 = two molecules of UO2
in.water = eight water molecules
** run 2 executables with TCP/IP, 1 proc each
** run LAMMPS and LATTE with TCP/IP, 1 proc each
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.tcp.1 -in in.water &
python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.water
@ -115,7 +123,7 @@ python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostn
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.series.tcp.1 -in in.series &
python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.uo2
** run 2 executables with MPI, 1 proc each
** run LAMMPS and LATTE with MPI, 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.mpi.1 -in in.water : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.water
@ -131,7 +139,7 @@ mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.graphene
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.series.mpi.1 -in in.series : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.uo2
** run LATTE as plugin MDI engine, on 1 proc
** run LATTE as plugin MDI engine, 1 proc
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.water.plugin.1 -in in.water.plugin

98
examples/QUANTUM/NWChem/README
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@ -1,18 +1,17 @@
# Test runs of QMMM with LAMMPS and NWChem
# Test runs with coupling of LAMMPS and NWChem PWDFT
Step 1: build LAMMPS
Step 2: download/build the MDI code coupling package
Step 2: download/build MDI code coupling package
Step 3: download/build NWChem PWDFT
Step 4: run 2-water QMMM problem for a few steps
Step 4: perform test runs in any of 3 modes
---------------------------------
---------------------------------
Step 1: build LAMMPS
The molecule package is needed for the 2-water test
problem. Copy the final LAMMPS executable into the
examples/QUANTUM/NWChem directory.
The MDI and molecule packags are needed. Copy the final LAMMPS
executable into the examples/QUANTUM/NWChem directory.
Traditional make:
@ -27,16 +26,16 @@ CMake:
% cd ~/lammps
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
% cmake -DPKG_MDI=yes -DPKG_MOLECULE=yes ../cmake
% make -j
% cp lmp ~/lammps/examples/QUANTUM/NWChem/lmp_mpi
---------------------------------
---------------------------------
Step 2: install the MDI code coupling package
Step 2: download/build MDI code coupling package
(a) grab the MDI Git repo
(a) clone the MDI Git repo
% mkdir mdi; cd mdi
% git clone git@github.com:MolSSI-MDI/MDI_Library.git git
@ -48,8 +47,8 @@ Step 2: install the MDI code coupling package
% cmake ..
% make -j
(c) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find MDI:
(c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that
Python can find MDI:
For bash:
@ -61,8 +60,8 @@ For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git
% rehash
(d) Check that you can import the 3 Python modules which the script
that wraps PySCF will need:
(d) Check import of 3 Python modules which the script that wraps
NWChem will need:
% python
>>> import numpy as np
@ -74,20 +73,20 @@ that wraps PySCF will need:
Step 3: download/build NWChem PWDFT
(a) grab the PWDFT Git repo
(a) clone the PWDFT Git repo
% mkdir nwchem; cd nwchem
% git clone git@github.com:ebylaska/PWDFT.git PWDFT
(b) build PWDFT
% cd nwchem/PWDFT
% cd ~/nwchem/PWDFT
% cd build_library; rm -r *
% cmake ../Nwpw -DMAKE_LIBRARY=true -DCMAKE_POSITION_INDEPENDENT_CODE=ON
% cmake -DMAKE_LIBRARY=true -DCMAKE_POSITION_INDEPENDENT_CODE=ON ../Nwpw
% make -j # should produce libpwdft.so in build_library
(c) Add something similar to the following to your .bashrc or .cshrc
file so that the Python wrapper script can find libpwdft.so:
(c) Add a line like this to your ~/.bashrc or !/.cshrc
file so that the libpwdft.so file can be found:
For bash:
@ -102,56 +101,43 @@ For (t)csh:
---------------------------------
---------------------------------
Step 4: run the 2-water QMMM problem for a few steps
Step 4: perform test runs in any of 3 modes
% cd ~/lammps/examples/QUANTUM/NWChem
These tests are in lammps/examples/QUANTUM/NWChem
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water,qmmm.tcp.1 -in in.water.qmmm &
in.series = series of several W conformations
in.water.qmmm = QMMM of two-water system, one QM + 1 MM
in.zeolite.qmmm = QMMM of zeolite (MM0 with a methane (QM) molecule
python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.water.nw water.dimer.nw log.water.pwdft.qmmm.tcp.1
** run LAMMPS-only versions of water and zeolite problems
# Run with MPI: 1 proc each
lmp_mpi -log log.water.mm.1 < in.water.mm
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.qmmm.mpi.1 -in in.water.qmmm : -np 1 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.water.nw water.dimer.nw log.water.pwdft.qmmm.mpi.1
lmp_mpi -log log.zeolite.mm.1 < in.zeolite.mm
# Run in plugin mode: 1 proc
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.water.qmmm.plugin.1 -in in.water.qmmm.plugin
---------------------------------
---------------------------------
Step 5: run the zeolite/methane QMMM problem for a few steps
% cd ~/lammps/examples/QUANTUM/NWChem
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.zeolite.qmmm.tcp.1 -in in.zeolite.qmmm &
python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.tcp.1
# Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.zeolite.qmmm.mpi.1 -in in.zeolite.qmmm : -np 1 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.mpi.1
# Run in plugin mode: 1 proc
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.zeolite.qmmm.plugin.1 -in in.zeolite.qmmm.plugin
---------------------------------
---------------------------------
Step 6: run multiple W geometries
% cd ~/lammps/examples/QUANTUM/NWChem
** run LAMMPS and PWDFT with TCP/IP, 1 or more procs each
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.series.tcp.1 -in in.series &
python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.w.nw w.nw log.series.pwdft.tcp.1
# Run with MPI: 1 proc each
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.qmmm.tcp.1 -in in.water.qmmm &
mpirun -np 2 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.water.nw water.nw log.water.pwdft.qmmm.tcp.2
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.zeolite.qmmm.tcp.1 -in in.zeolite.qmmm &
mpirun -np 8 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.tcp.8
** run LAMMPS and PWDFT with MPI, 1 or more procs each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.series.mpi.1 -in in.series : -np 1 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.w.nw w.nw log.series.pwdft.mpi.1
# Run in plugin mode: 1 proc
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.qmmm.mpi.1 -in in.water.qmmm : -np 2 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.water.nw water.nw log.water.pwdft.qmmm.mpi.2
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.zeolite.qmmm.mpi.1 -in in.zeolite.qmmm : -np 8 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.mpi.8
** run PWDFT as plugin MDI engine, 1 or more procs
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.series.plugin.1 -in in.series.plugin
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.water.qmmm.plugin.2 -in in.water.qmmm.plugin
mpirun -np 8 lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.zeolite.qmmm.plugin.8 -in in.zeolite.qmmm.plugin

12
examples/QUANTUM/NWChem/in.series
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@ -1,6 +1,10 @@
# multiple W conformations with NWChem
variable datafile index data.w.bcc data.w.diamond
# NOTE: these files still need work with PWDFT
# w.bcc_222, w.fcc_001, w.sc_001
variable datafile index w.bcc w.diamond
variable p equal extract_setting(world_size)
mdi connect
@ -11,9 +15,9 @@ label loop
atom_modify map yes
comm_modify cutoff 2.0
log log.series.${datafile}
log log.series.${datafile}.$p
read_data ${datafile}
read_data data.${datafile}
mass 1 183.84
@ -23,7 +27,7 @@ label loop
fix 1 all mdi/qm elements W connect no
fix_modify 1 energy yes
dump 1 all custom 1 dump.series.${datafile} id x y z fx fy fz
#dump 1 all custom 1 dump.series.${datafile}.$p id x y z fx fy fz
run 0

14
examples/QUANTUM/NWChem/in.series.plugin
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@ -1,6 +1,10 @@
# multiple W conformations with NWChem
variable datafile index data.w.bcc data.w.diamond
# NOTE: these files still need work with PWDFT
# w.bcc_222, w.fcc_001, w.sc_001
variable datafile index w.bcc w.diamond
variable p equal extract_setting(world_size)
label loop
@ -9,9 +13,9 @@ label loop
atom_modify map yes
comm_modify cutoff 2.0
log log.series.plugin.${datafile}
log log.series.plugin.${datafile}.$p
read_data ${datafile}
read_data data.${datafile}
mass 1 183.84
@ -21,10 +25,10 @@ label loop
fix 1 all mdi/qm elements W
fix_modify 1 energy yes
dump 1 all custom 1 dump.series.plugin.${datafile} id x y z fx fy fz
#dump 1 all custom 1 dump.series.plugin.${datafile} id x y z fx fy fz
mdi plugin nwchem_mdi mdi "-role ENGINE -name LATTE -method LINK" &
extra "template.w.nw w.nw log.series.pwdft.plugin.1" &
extra "template.w.nw w.nw log.series.pwdft.plugin.$p" &
command "run 0"
clear

4
examples/QUANTUM/NWChem/in.water.qmmm.plugin
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@ -56,6 +56,8 @@ thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
f_2 pe etotal press
thermo 1
variable p equal extract_setting(world_size)
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" &
extra "template.water.nw water.dimer.nw log.water.pwdft.qmmm.plugin.1" &
extra "template.water.nw water.dimer.nw log.water.pwdft.qmmm.plugin.$p" &
command "run 1"

4
examples/QUANTUM/NWChem/in.zeolite.qmmm.plugin
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@ -67,6 +67,8 @@ thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
f_2 pe etotal press
thermo 1
variable p equal extract_setting(world_size)
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" &
extra "template.methane.nw methane.nw log.zeolite.pwdft.qmmm.plugin.1" &
extra "template.methane.nw methane.nw log.zeolite.pwdft.qmmm.plugin.$p" &
command "run 2"

21
examples/QUANTUM/NWChem/log.8Feb23.series.mpi.1 Normal file
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@ -0,0 +1,21 @@
LAMMPS (22 Dec 2022)
# multiple W conformations with NWChem
# NOTE: these files still need work with PWDFT
# w.bcc_222, w.fcc_001, w.sc_001
variable datafile index w.bcc w.diamond
variable p equal extract_setting(world_size)
mdi connect
label loop
units metal
atom_style atomic
atom_modify map yes
comm_modify cutoff 2.0
log log.series.${datafile}.$p
log log.series.w.bcc.$p
log log.series.w.bcc.1

19
examples/QUANTUM/NWChem/log.8Feb23.series.plugin.1 Normal file
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@ -0,0 +1,19 @@
LAMMPS (22 Dec 2022)
# multiple W conformations with NWChem
# NOTE: these files still need work with PWDFT
# w.bcc_222, w.fcc_001, w.sc_001
variable datafile index w.bcc w.diamond
variable p equal extract_setting(world_size)
label loop
units metal
atom_style atomic
atom_modify map yes
comm_modify cutoff 2.0
log log.series.plugin.${datafile}.$p
log log.series.plugin.w.bcc.$p
log log.series.plugin.w.bcc.1

67
examples/QUANTUM/NWChem/log.8Feb23.series.plugin.w.bcc.1 Normal file
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@ -0,0 +1,67 @@
read_data data.${datafile}
read_data data.w.bcc
Reading data file ...
orthogonal box = (0 0 0) to (3.1654062 3.1654062 3.1654062)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
read_data CPU = 0.001 seconds
mass 1 183.84
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm elements W
fix_modify 1 energy yes
#dump 1 all custom 1 dump.series.plugin.${datafile} id x y z fx fy fz
mdi plugin nwchem_mdi mdi "-role ENGINE -name LATTE -method LINK" extra "template.w.nw w.nw log.series.pwdft.plugin.$p" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
Per MPI rank memory allocation (min/avg/max) = 2.301 | 2.301 | 2.301 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 -577.92971 2.3613806e-305
Loop time of 8.46e-07 on 1 procs for 0 steps with 2 atoms
118.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 8.46e-07 | | |100.00
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 33 ave 33 max 33 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
clear
next datafile
jump SELF loop
units metal
atom_style atomic
atom_modify map yes
comm_modify cutoff 2.0
log log.series.plugin.${datafile}.$p
log log.series.plugin.w.diamond.$p
log log.series.plugin.w.diamond.1

59
examples/QUANTUM/NWChem/log.8Feb23.series.plugin.w.diamond.1 Normal file
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@ -0,0 +1,59 @@
read_data data.${datafile}
read_data data.w.diamond
Reading data file ...
orthogonal box = (0 0 0) to (2.8200564 2.8200564 3.988162)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
read_data CPU = 0.000 seconds
mass 1 183.84
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm elements W
fix_modify 1 energy yes
#dump 1 all custom 1 dump.series.plugin.${datafile} id x y z fx fy fz
mdi plugin nwchem_mdi mdi "-role ENGINE -name LATTE -method LINK" extra "template.w.nw w.nw log.series.pwdft.plugin.$p" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
Per MPI rank memory allocation (min/avg/max) = 2.301 | 2.301 | 2.301 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 -1052.9159 2.3613806e-305
Loop time of 5.96e-07 on 1 procs for 0 steps with 4 atoms
167.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 5.96e-07 | | |100.00
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 55 ave 55 max 55 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
clear
next datafile
jump SELF loop
Total wall time: 0:00:00

725
examples/QUANTUM/NWChem/log.8Feb23.series.pwdft.mpi.1 Normal file
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@ -0,0 +1,725 @@
*****************************************************
* *
* 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 Wed Feb 8 15:54:30 2023 <<<
psp_library: /home/sjplimp/nwchem/PWDFT/Nwpw/libraryps
writing formatted psp filename: ./W.vpp
generating random psi from scratch
Warning - Gram-Schmidt being performed on psi2
- exact norm = 12 norm=12.4399 corrected norm=12 (error=0.439878)
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 1
processor grid : 1 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: W valence charge = 6.0 lmax =2
comment = Troullier-Martins pseudopotential
pseudopotential type = 0
highest angular component = 2
local potential used = 0
number of non-local projections = 8
semicore corrections inlcuded = 1.800 (radius) 4.532 (charge)
cutoff = 2.389 3.185 2.244
total charge = 0.000
atom composition:
W : 2
initial ion positions (au):
1 W ( 0.00000 0.00000 0.00000 ) - atomic mass = 183.951
2 W ( 2.99088 2.99088 2.99088 ) - atomic mass = 183.951
G.C. ( 1.49544 1.49544 1.49544 )
C.O.M. ( 1.49544 1.49544 1.49544 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 6 ( 6 per task) down = 6 ( 6 per task)
supercell:
volume = 214.04
lattice: a1 = < 5.982 0.000 0.000 >
a2 = < 0.000 5.982 0.000 >
a3 = < 0.000 0.000 5.982 >
reciprocal: b1 = < 1.050 0.000 0.000 >
b2 = < 0.000 1.050 0.000 >
b3 = < 0.000 0.000 1.050 >
lattice: a = 5.982 b = 5.982 c = 5.982
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 10.000 fft = 10 x 10 x 10 ( 171 waves 171 per task)
wavefnc cutoff = 5.000 fft = 10 x 10 x 10 ( 62 waves 62 per task)
Ewald parameters:
energy cutoff = 10.000 fft = 10 x 10 x 10 ( 171 waves 171 per task)
Ewald summation: cut radius = 1.904 and 1
Mandelung Wigner-Seitz = 1.76011888 (alpha = 2.83729748 rs = 3.71078182)
technical parameters:
fixed step: 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 Wed Feb 8 15:54:30 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -1.708816420389e+01 -2.241680e-01 2.492794e-03
20 -1.905311322397e+01 -1.075101e-01 9.399452e-04
30 -1.958772952424e+01 -4.100623e-02 3.486639e-04
40 -1.998528675502e+01 -3.159736e-02 2.833077e-04
50 -2.015674839165e+01 -1.012189e-03 3.920512e-05
60 -2.015924714018e+01 -9.524059e-05 3.548660e-05
70 -2.015944170667e+01 -1.607819e-05 5.414864e-06
80 -2.015946503285e+01 -8.423156e-07 1.645114e-07
90 -2.015946835363e+01 -1.954822e-07 3.754719e-08
100 -2.015946869692e+01 -9.810346e-08 4.474449e-09
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:54:31 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 5.00000 down= 5.00000 (real space)
total energy : -2.0159468697e+01 ( -1.00797e+01 /ion)
total orbital energy: 5.1058644255e+00 ( 8.50977e-01 /electron)
hartree energy : 8.5016689728e-02 ( 1.41694e-02 /electron)
exc-corr energy : -8.1926599847e+00 ( -1.36544e+00 /electron)
ion-ion energy : -2.1902017710e+01 ( -1.09510e+01 /ion)
kinetic (planewave) : 9.2934723839e+00 ( 1.54891e+00 /electron)
V_local (planewave) : 8.1075657962e+00 ( 1.35126e+00 /electron)
V_nl (planewave) : -7.5508458716e+00 ( -1.25847e+00 /electron)
V_Coul (planewave) : 1.7003337946e-01 ( 2.83389e-02 /electron)
V_xc (planewave) : -4.9143612625e+00 ( -8.19060e-01 /electron)
Viral Coefficient : -4.5059669684e-01
orbital energy:
6.7894851e-01 ( 18.475eV)
6.7894804e-01 ( 18.475eV)
4.7881075e-01 ( 13.029eV)
4.6795217e-01 ( 12.734eV)
2.4827275e-01 ( 6.756eV)
1.2228165e-09 ( 0.000eV)
== Center of Charge ==
spin up = ( -0.0000 0.0000 -0.0000 )
spin down = ( -0.0000 0.0000 -0.0000 )
total = ( -0.0000 0.0000 -0.0000 )
ionic = ( 1.4954 1.4954 1.4954 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 17.9453 17.9452 17.9453 ) au
|mu| = 31.0821 au ( 78.9982 Debye )
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 2.907e-02
main loop : 1.004e-01
epilogue : 1.870e-04
total : 1.297e-01
cputime/step: 3.304e-04 ( 304 evaluations, 93 linesearches)
Time spent doing total step percent
total time 1.322631e-01 4.350761e-04 100.00%
total FFT time 4.995464e-02 1.643245e-04 37.77%
lagrange multipliers 5.076800e-05 1.670000e-07 0.04%
local potentials 3.725000e-06 1.225329e-08 0.00%
non-local potentials 1.856634e-03 6.107349e-06 1.40%
ffm_dgemm 6.068270e-04 1.996141e-06 0.46%
fmf_dgemm 1.002816e-03 3.298737e-06 0.76%
m_diagonalize 3.252760e-04 1.069987e-06 0.25%
mmm_multiply 8.684300e-05 2.856678e-07 0.07%
SCVtrans 6.873300e-05 2.260954e-07 0.05%
>>> job completed at Wed Feb 8 15:54:31 2023 <<<
*****************************************************
* *
* 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 Wed Feb 8 15:54:31 2023 <<<
psp_library: /home/sjplimp/nwchem/PWDFT/Nwpw/libraryps
writing formatted psp filename: ./W.vpp
psi grids are being converted:
-----------------------------:
converting .... psi:1 spin:1
converting .... psi:2 spin:1
converting .... psi:3 spin:1
converting .... psi:4 spin:1
converting .... psi:5 spin:1
converting .... psi:6 spin:1
input psi exists, reading from file: ./nwchemex.movecs
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 1
processor grid : 1 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: W valence charge = 6.0 lmax =2
comment = Troullier-Martins pseudopotential
pseudopotential type = 0
highest angular component = 2
local potential used = 0
number of non-local projections = 8
semicore corrections inlcuded = 1.800 (radius) 4.536 (charge)
cutoff = 2.389 3.185 2.244
total charge = 0.000
atom composition:
W : 2
initial ion positions (au):
1 W ( 0.00000 0.00000 0.00000 ) - atomic mass = 183.951
2 W ( 2.99088 2.99088 2.99088 ) - atomic mass = 183.951
G.C. ( 1.49544 1.49544 1.49544 )
C.O.M. ( 1.49544 1.49544 1.49544 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 6 ( 6 per task) down = 6 ( 6 per task)
supercell:
volume = 214.04
lattice: a1 = < 5.982 0.000 0.000 >
a2 = < 0.000 5.982 0.000 >
a3 = < 0.000 0.000 5.982 >
reciprocal: b1 = < 1.050 0.000 0.000 >
b2 = < 0.000 1.050 0.000 >
b3 = < 0.000 0.000 1.050 >
lattice: a = 5.982 b = 5.982 c = 5.982
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 20.000 fft = 14 x 14 x 14 ( 463 waves 463 per task)
wavefnc cutoff = 10.000 fft = 14 x 14 x 14 ( 171 waves 171 per task)
Ewald parameters:
energy cutoff = 20.000 fft = 14 x 14 x 14 ( 463 waves 463 per task)
Ewald summation: cut radius = 1.904 and 1
Mandelung Wigner-Seitz = 1.76011888 (alpha = 2.83729748 rs = 3.71078182)
technical parameters:
fixed step: 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 Wed Feb 8 15:54:31 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -2.123852173470e+01 -1.701822e-06 1.823996e-08
20 -2.123852523532e+01 -1.768295e-08 1.488081e-10
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:54:31 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 5.00000 down= 5.00000 (real space)
total energy : -2.1238525235e+01 ( -1.06193e+01 /ion)
total orbital energy: 4.1856287995e+00 ( 6.97605e-01 /electron)
hartree energy : 1.8249301478e-01 ( 3.04155e-02 /electron)
exc-corr energy : -8.4273499426e+00 ( -1.40456e+00 /electron)
ion-ion energy : -2.1902017722e+01 ( -1.09510e+01 /ion)
kinetic (planewave) : 1.1347791251e+01 ( 1.89130e+00 /electron)
V_local (planewave) : 9.5182220550e+00 ( 1.58637e+00 /electron)
V_nl (planewave) : -1.1957663891e+01 ( -1.99294e+00 /electron)
V_Coul (planewave) : 3.6498602956e-01 ( 6.08310e-02 /electron)
V_xc (planewave) : -5.0877066444e+00 ( -8.47951e-01 /electron)
Viral Coefficient : -6.3115035278e-01
orbital energy:
5.4500741e-01 ( 14.831eV)
5.4500728e-01 ( 14.831eV)
3.8896747e-01 ( 10.584eV)
3.7572955e-01 ( 10.224eV)
2.3810268e-01 ( 6.479eV)
-1.0451709e-16 ( -0.000eV)
== Center of Charge ==
spin up = ( -0.0000 -0.0000 -0.0000 )
spin down = ( -0.0000 -0.0000 -0.0000 )
total = ( -0.0000 -0.0000 -0.0000 )
ionic = ( 1.4954 1.4954 1.4954 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 17.9453 17.9453 17.9453 ) au
|mu| = 31.0821 au ( 78.9982 Debye )
Ion Forces (au):
1 W ( -0.00000 0.00000 0.00000 )
2 W ( -0.00000 -0.00000 0.00000 )
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 3.769e-02
main loop : 7.563e-02
epilogue : 6.960e-04
total : 1.140e-01
cputime/step: 1.260e-03 ( 60 evaluations, 16 linesearches)
Time spent doing total step percent
total time 2.465272e-01 4.108787e-03 100.00%
total FFT time 9.983296e-02 1.663883e-03 40.50%
lagrange multipliers 1.398700e-04 2.331167e-06 0.06%
local potentials 1.354200e-05 2.257000e-07 0.01%
non-local potentials 2.966487e-03 4.944145e-05 1.20%
ffm_dgemm 8.991500e-04 1.498583e-05 0.36%
fmf_dgemm 1.509976e-03 2.516627e-05 0.61%
m_diagonalize 4.034020e-04 6.723367e-06 0.16%
mmm_multiply 1.026590e-04 1.710983e-06 0.04%
SCVtrans 8.243300e-05 1.373883e-06 0.03%
>>> job completed at Wed Feb 8 15:54:31 2023 <<<
*****************************************************
* *
* 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 Wed Feb 8 15:54:31 2023 <<<
psp_library: /home/sjplimp/nwchem/PWDFT/Nwpw/libraryps
writing formatted psp filename: ./W.vpp
generating random psi from scratch
Warning - Gram-Schmidt being performed on psi2
- exact norm = 24 norm=24.6534 corrected norm=24 (error=0.65341)
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 1
processor grid : 1 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: W valence charge = 6.0 lmax =2
comment = Troullier-Martins pseudopotential
pseudopotential type = 0
highest angular component = 2
local potential used = 0
number of non-local projections = 8
semicore corrections inlcuded = 1.800 (radius) 4.591 (charge)
cutoff = 2.389 3.185 2.244
total charge = 0.000
atom composition:
W : 4
initial ion positions (au):
1 W ( 0.00000 0.00000 0.00000 ) - atomic mass = 183.951
2 W ( 2.66457 0.00000 1.88413 ) - atomic mass = 183.951
3 W ( 2.66457 2.66457 3.76827 ) - atomic mass = 183.951
4 W ( 0.00000 2.66457 5.65240 ) - atomic mass = 183.951
G.C. ( 1.33228 1.33228 2.82620 )
C.O.M. ( 1.33228 1.33228 2.82620 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 12 ( 12 per task) down = 12 ( 12 per task)
supercell:
volume = 214.04
lattice: a1 = < 5.329 0.000 0.000 >
a2 = < 0.000 5.329 0.000 >
a3 = < 0.000 0.000 7.537 >
reciprocal: b1 = < 1.179 0.000 0.000 >
b2 = < 0.000 1.179 0.000 >
b3 = < 0.000 0.000 0.834 >
lattice: a = 5.329 b = 5.329 c = 7.537
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 10.000 fft = 10 x 10 x 12 ( 160 waves 160 per task)
wavefnc cutoff = 5.000 fft = 10 x 10 x 12 ( 62 waves 62 per task)
Ewald parameters:
energy cutoff = 10.000 fft = 10 x 10 x 12 ( 160 waves 160 per task)
Ewald summation: cut radius = 1.696 and 1
Mandelung Wigner-Seitz = 1.68382487 (alpha = 2.71431215 rs = 3.71078182)
technical parameters:
fixed step: 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 Wed Feb 8 15:54:31 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -3.263325288087e+01 -2.370052e-01 2.755915e-03
20 -3.342232241827e+01 -5.863540e-02 2.971603e-04
30 -3.391324997303e+01 -3.187197e-02 1.546984e-04
40 -3.413597312443e+01 -2.155176e-02 1.238590e-04
50 -3.438373510198e+01 -2.450980e-02 1.027256e-04
60 -3.455017548679e+01 -9.891297e-03 4.618600e-05
70 -3.464713762751e+01 -1.297081e-03 6.690651e-05
80 -3.465330146645e+01 -8.056294e-04 7.652741e-04
90 -3.466599502278e+01 -8.084057e-04 1.644931e-04
100 -3.466738274142e+01 -4.655569e-05 6.208520e-06
110 -3.466755259026e+01 -6.106702e-06 9.485566e-07
120 -3.466757480938e+01 -5.729432e-07 6.423950e-08
130 -3.466757780500e+01 -9.928726e-08 1.501512e-08
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:54:31 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 11.00000 down= 11.00000 (real space)
total energy : -3.4667577805e+01 ( -8.66689e+00 /ion)
total orbital energy: 2.4064172121e+01 ( 2.00535e+00 /electron)
hartree energy : 6.5304190697e-01 ( 5.44202e-02 /electron)
exc-corr energy : -2.0726372095e+01 ( -1.72720e+00 /electron)
ion-ion energy : -5.1462578555e+01 ( -1.28656e+01 /ion)
kinetic (planewave) : 3.2744878583e+01 ( 2.72874e+00 /electron)
V_local (planewave) : 3.5170322604e+01 ( 2.93086e+00 /electron)
V_nl (planewave) : -3.1046870249e+01 ( -2.58724e+00 /electron)
V_Coul (planewave) : 1.3060838139e+00 ( 1.08840e-01 /electron)
V_xc (planewave) : -1.4110242631e+01 ( -1.17585e+00 /electron)
Viral Coefficient : -2.6510119560e-01
orbital energy:
1.4424311e+00 ( 39.251eV)
1.2160817e+00 ( 33.092eV)
1.2090712e+00 ( 32.901eV)
1.2054584e+00 ( 32.802eV)
1.1963001e+00 ( 32.553eV)
1.1954706e+00 ( 32.531eV)
9.9977937e-01 ( 27.206eV)
9.9502181e-01 ( 27.076eV)
8.8723317e-01 ( 24.143eV)
8.8678761e-01 ( 24.131eV)
7.9845106e-01 ( 21.727eV)
4.8910438e-09 ( 0.000eV)
== Center of Charge ==
spin up = ( -0.0000 -0.0000 -0.0252 )
spin down = ( -0.0000 -0.0000 -0.0252 )
total = ( -0.0000 -0.0000 -0.0252 )
ionic = ( 1.3323 1.3323 2.8262 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 31.9757 31.9749 68.4348 ) au
|mu| = 82.0253 au ( 208.4756 Debye )
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 3.574e-02
main loop : 2.296e-01
epilogue : 2.510e-04
total : 2.656e-01
cputime/step: 5.506e-04 ( 417 evaluations, 130 linesearches)
Time spent doing total step percent
total time 5.140170e-01 1.232655e-03 100.00%
total FFT time 2.234995e-01 5.359700e-04 43.48%
lagrange multipliers 3.276480e-04 7.857266e-07 0.06%
local potentials 1.836000e-05 4.402878e-08 0.00%
non-local potentials 1.061595e-02 2.545792e-05 2.07%
ffm_dgemm 3.946196e-03 9.463300e-06 0.77%
fmf_dgemm 6.759673e-03 1.621025e-05 1.32%
m_diagonalize 2.016443e-03 4.835595e-06 0.39%
mmm_multiply 4.805990e-04 1.152516e-06 0.09%
SCVtrans 2.609230e-04 6.257146e-07 0.05%
>>> job completed at Wed Feb 8 15:54:31 2023 <<<
*****************************************************
* *
* 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 Wed Feb 8 15:54:31 2023 <<<
psp_library: /home/sjplimp/nwchem/PWDFT/Nwpw/libraryps
writing formatted psp filename: ./W.vpp
psi grids are being converted:
-----------------------------:
converting .... psi:1 spin:1
converting .... psi:2 spin:1
converting .... psi:3 spin:1
converting .... psi:4 spin:1
converting .... psi:5 spin:1
converting .... psi:6 spin:1
converting .... psi:7 spin:1
converting .... psi:8 spin:1
converting .... psi:9 spin:1
converting .... psi:10 spin:1
converting .... psi:11 spin:1
converting .... psi:12 spin:1
input psi exists, reading from file: ./nwchemex.movecs
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 1
processor grid : 1 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: W valence charge = 6.0 lmax =2
comment = Troullier-Martins pseudopotential
pseudopotential type = 0
highest angular component = 2
local potential used = 0
number of non-local projections = 8
semicore corrections inlcuded = 1.800 (radius) 4.595 (charge)
cutoff = 2.389 3.185 2.244
total charge = 0.000
atom composition:
W : 4
initial ion positions (au):
1 W ( 0.00000 0.00000 0.00000 ) - atomic mass = 183.951
2 W ( 2.66457 0.00000 1.88413 ) - atomic mass = 183.951
3 W ( 2.66457 2.66457 3.76827 ) - atomic mass = 183.951
4 W ( 0.00000 2.66457 5.65240 ) - atomic mass = 183.951
G.C. ( 1.33228 1.33228 2.82620 )
C.O.M. ( 1.33228 1.33228 2.82620 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 12 ( 12 per task) down = 12 ( 12 per task)
supercell:
volume = 214.04
lattice: a1 = < 5.329 0.000 0.000 >
a2 = < 0.000 5.329 0.000 >
a3 = < 0.000 0.000 7.537 >
reciprocal: b1 = < 1.179 0.000 0.000 >
b2 = < 0.000 1.179 0.000 >
b3 = < 0.000 0.000 0.834 >
lattice: a = 5.329 b = 5.329 c = 7.537
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 20.000 fft = 12 x 12 x 16 ( 460 waves 460 per task)
wavefnc cutoff = 10.000 fft = 12 x 12 x 16 ( 160 waves 160 per task)
Ewald parameters:
energy cutoff = 20.000 fft = 12 x 12 x 16 ( 460 waves 460 per task)
Ewald summation: cut radius = 1.696 and 1
Mandelung Wigner-Seitz = 1.68382487 (alpha = 2.71431215 rs = 3.71078182)
technical parameters:
fixed step: 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 Wed Feb 8 15:54:31 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -3.869390116272e+01 -6.903668e-05 1.222538e-06
20 -3.869394600954e+01 -2.584005e-08 7.565630e-10
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:54:31 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 11.00000 down= 11.00000 (real space)
total energy : -3.8693946010e+01 ( -9.67349e+00 /ion)
total orbital energy: 2.0571849938e+01 ( 1.71432e+00 /electron)
hartree energy : 1.0464327958e+00 ( 8.72027e-02 /electron)
exc-corr energy : -2.1151466566e+01 ( -1.76262e+00 /electron)
ion-ion energy : -5.1462581523e+01 ( -1.28656e+01 /ion)
kinetic (planewave) : 3.7980397820e+01 ( 3.16503e+00 /electron)
V_local (planewave) : 3.8936852411e+01 ( 3.24474e+00 /electron)
V_nl (planewave) : -4.4043580948e+01 ( -3.67030e+00 /electron)
V_Coul (planewave) : 2.0928655917e+00 ( 1.74405e-01 /electron)
V_xc (planewave) : -1.4394684937e+01 ( -1.19956e+00 /electron)
Viral Coefficient : -4.5835612267e-01
orbital energy:
1.2624273e+00 ( 34.353eV)
1.0588423e+00 ( 28.813eV)
1.0519217e+00 ( 28.624eV)
1.0510387e+00 ( 28.600eV)
1.0124484e+00 ( 27.550eV)
1.0116561e+00 ( 27.529eV)
7.9997475e-01 ( 21.769eV)
7.9985716e-01 ( 21.765eV)
7.5624184e-01 ( 20.579eV)
7.4126320e-01 ( 20.171eV)
7.4025353e-01 ( 20.143eV)
1.6826541e-12 ( 0.000eV)
== Center of Charge ==
spin up = ( -0.0000 -0.0000 -0.0237 )
spin down = ( -0.0000 -0.0000 -0.0237 )
total = ( -0.0000 -0.0000 -0.0237 )
ionic = ( 1.3323 1.3323 2.8262 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 31.9750 31.9748 68.3970 ) au
|mu| = 81.9935 au ( 208.3948 Debye )
Ion Forces (au):
1 W ( -0.00005 -0.00003 0.52530 )
2 W ( 0.00004 0.00003 -0.52538 )
3 W ( 0.00004 0.00002 0.52530 )
4 W ( -0.00005 -0.00002 -0.52538 )
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 4.245e-02
main loop : 6.749e-02
epilogue : 8.180e-04
total : 1.108e-01
cputime/step: 1.007e-03 ( 67 evaluations, 18 linesearches)
Time spent doing total step percent
total time 6.250279e-01 9.328775e-03 100.00%
total FFT time 2.586332e-01 3.860197e-03 41.38%
lagrange multipliers 6.249210e-04 9.327179e-06 0.10%
local potentials 3.540200e-05 5.283881e-07 0.01%
non-local potentials 1.400041e-02 2.089614e-04 2.24%
ffm_dgemm 5.165183e-03 7.709228e-05 0.83%
fmf_dgemm 8.843997e-03 1.320000e-04 1.41%
m_diagonalize 2.293617e-03 3.423309e-05 0.37%
mmm_multiply 5.365630e-04 8.008403e-06 0.09%
SCVtrans 2.880560e-04 4.299343e-06 0.05%
>>> job completed at Wed Feb 8 15:54:31 2023 <<<

725
examples/QUANTUM/NWChem/log.8Feb23.series.pwdft.plugin.1 Normal file
View File

@ -0,0 +1,725 @@
*****************************************************
* *
* 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 Wed Feb 8 15:50:51 2023 <<<
psp_library: /home/sjplimp/nwchem/PWDFT/Nwpw/libraryps
writing formatted psp filename: ./W.vpp
generating random psi from scratch
Warning - Gram-Schmidt being performed on psi2
- exact norm = 12 norm=12.4399 corrected norm=12 (error=0.439878)
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 1
processor grid : 1 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: W valence charge = 6.0 lmax =2
comment = Troullier-Martins pseudopotential
pseudopotential type = 0
highest angular component = 2
local potential used = 0
number of non-local projections = 8
semicore corrections inlcuded = 1.800 (radius) 4.532 (charge)
cutoff = 2.389 3.185 2.244
total charge = 0.000
atom composition:
W : 2
initial ion positions (au):
1 W ( 0.00000 0.00000 0.00000 ) - atomic mass = 183.951
2 W ( 2.99088 2.99088 2.99088 ) - atomic mass = 183.951
G.C. ( 1.49544 1.49544 1.49544 )
C.O.M. ( 1.49544 1.49544 1.49544 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 6 ( 6 per task) down = 6 ( 6 per task)
supercell:
volume = 214.04
lattice: a1 = < 5.982 0.000 0.000 >
a2 = < 0.000 5.982 0.000 >
a3 = < 0.000 0.000 5.982 >
reciprocal: b1 = < 1.050 0.000 0.000 >
b2 = < 0.000 1.050 0.000 >
b3 = < 0.000 0.000 1.050 >
lattice: a = 5.982 b = 5.982 c = 5.982
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 10.000 fft = 10 x 10 x 10 ( 171 waves 171 per task)
wavefnc cutoff = 5.000 fft = 10 x 10 x 10 ( 62 waves 62 per task)
Ewald parameters:
energy cutoff = 10.000 fft = 10 x 10 x 10 ( 171 waves 171 per task)
Ewald summation: cut radius = 1.904 and 1
Mandelung Wigner-Seitz = 1.76011888 (alpha = 2.83729748 rs = 3.71078182)
technical parameters:
fixed step: 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 Wed Feb 8 15:50:51 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -1.708816420389e+01 -2.241680e-01 2.492794e-03
20 -1.905311322397e+01 -1.075101e-01 9.399452e-04
30 -1.958772952424e+01 -4.100623e-02 3.486639e-04
40 -1.998528675502e+01 -3.159736e-02 2.833077e-04
50 -2.015674839165e+01 -1.012189e-03 3.920512e-05
60 -2.015924714018e+01 -9.524059e-05 3.548660e-05
70 -2.015944170667e+01 -1.607819e-05 5.414864e-06
80 -2.015946503285e+01 -8.423156e-07 1.645114e-07
90 -2.015946835363e+01 -1.954822e-07 3.754719e-08
100 -2.015946869692e+01 -9.810346e-08 4.474449e-09
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:50:51 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 5.00000 down= 5.00000 (real space)
total energy : -2.0159468697e+01 ( -1.00797e+01 /ion)
total orbital energy: 5.1058644255e+00 ( 8.50977e-01 /electron)
hartree energy : 8.5016689728e-02 ( 1.41694e-02 /electron)
exc-corr energy : -8.1926599847e+00 ( -1.36544e+00 /electron)
ion-ion energy : -2.1902017710e+01 ( -1.09510e+01 /ion)
kinetic (planewave) : 9.2934723839e+00 ( 1.54891e+00 /electron)
V_local (planewave) : 8.1075657962e+00 ( 1.35126e+00 /electron)
V_nl (planewave) : -7.5508458716e+00 ( -1.25847e+00 /electron)
V_Coul (planewave) : 1.7003337946e-01 ( 2.83389e-02 /electron)
V_xc (planewave) : -4.9143612625e+00 ( -8.19060e-01 /electron)
Viral Coefficient : -4.5059669684e-01
orbital energy:
6.7894851e-01 ( 18.475eV)
6.7894804e-01 ( 18.475eV)
4.7881075e-01 ( 13.029eV)
4.6795217e-01 ( 12.734eV)
2.4827275e-01 ( 6.756eV)
1.2228165e-09 ( 0.000eV)
== Center of Charge ==
spin up = ( -0.0000 0.0000 -0.0000 )
spin down = ( -0.0000 0.0000 -0.0000 )
total = ( -0.0000 0.0000 -0.0000 )
ionic = ( 1.4954 1.4954 1.4954 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 17.9453 17.9452 17.9453 ) au
|mu| = 31.0821 au ( 78.9982 Debye )
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 3.177e-01
main loop : 9.053e-02
epilogue : 3.190e-04
total : 4.086e-01
cputime/step: 2.978e-04 ( 304 evaluations, 93 linesearches)
Time spent doing total step percent
total time 1.350798e-01 4.443414e-04 100.00%
total FFT time 4.500482e-02 1.480422e-04 33.32%
lagrange multipliers 4.477900e-05 1.472993e-07 0.03%
local potentials 2.774000e-06 9.125000e-09 0.00%
non-local potentials 1.656622e-03 5.449414e-06 1.23%
ffm_dgemm 5.521080e-04 1.816145e-06 0.41%
fmf_dgemm 8.953870e-04 2.945352e-06 0.66%
m_diagonalize 3.079610e-04 1.013030e-06 0.23%
mmm_multiply 7.758400e-05 2.552105e-07 0.06%
SCVtrans 6.425500e-05 2.113651e-07 0.05%
>>> job completed at Wed Feb 8 15:50:51 2023 <<<
*****************************************************
* *
* 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 Wed Feb 8 15:50:51 2023 <<<
psp_library: /home/sjplimp/nwchem/PWDFT/Nwpw/libraryps
writing formatted psp filename: ./W.vpp
psi grids are being converted:
-----------------------------:
converting .... psi:1 spin:1
converting .... psi:2 spin:1
converting .... psi:3 spin:1
converting .... psi:4 spin:1
converting .... psi:5 spin:1
converting .... psi:6 spin:1
input psi exists, reading from file: ./nwchemex.movecs
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 1
processor grid : 1 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: W valence charge = 6.0 lmax =2
comment = Troullier-Martins pseudopotential
pseudopotential type = 0
highest angular component = 2
local potential used = 0
number of non-local projections = 8
semicore corrections inlcuded = 1.800 (radius) 4.536 (charge)
cutoff = 2.389 3.185 2.244
total charge = 0.000
atom composition:
W : 2
initial ion positions (au):
1 W ( 0.00000 0.00000 0.00000 ) - atomic mass = 183.951
2 W ( 2.99088 2.99088 2.99088 ) - atomic mass = 183.951
G.C. ( 1.49544 1.49544 1.49544 )
C.O.M. ( 1.49544 1.49544 1.49544 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 6 ( 6 per task) down = 6 ( 6 per task)
supercell:
volume = 214.04
lattice: a1 = < 5.982 0.000 0.000 >
a2 = < 0.000 5.982 0.000 >
a3 = < 0.000 0.000 5.982 >
reciprocal: b1 = < 1.050 0.000 0.000 >
b2 = < 0.000 1.050 0.000 >
b3 = < 0.000 0.000 1.050 >
lattice: a = 5.982 b = 5.982 c = 5.982
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 20.000 fft = 14 x 14 x 14 ( 463 waves 463 per task)
wavefnc cutoff = 10.000 fft = 14 x 14 x 14 ( 171 waves 171 per task)
Ewald parameters:
energy cutoff = 20.000 fft = 14 x 14 x 14 ( 463 waves 463 per task)
Ewald summation: cut radius = 1.904 and 1
Mandelung Wigner-Seitz = 1.76011888 (alpha = 2.83729748 rs = 3.71078182)
technical parameters:
fixed step: 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 Wed Feb 8 15:50:51 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -2.123852173470e+01 -1.701822e-06 1.823996e-08
20 -2.123852523532e+01 -1.768295e-08 1.488081e-10
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:50:51 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 5.00000 down= 5.00000 (real space)
total energy : -2.1238525235e+01 ( -1.06193e+01 /ion)
total orbital energy: 4.1856287995e+00 ( 6.97605e-01 /electron)
hartree energy : 1.8249301478e-01 ( 3.04155e-02 /electron)
exc-corr energy : -8.4273499426e+00 ( -1.40456e+00 /electron)
ion-ion energy : -2.1902017722e+01 ( -1.09510e+01 /ion)
kinetic (planewave) : 1.1347791251e+01 ( 1.89130e+00 /electron)
V_local (planewave) : 9.5182220550e+00 ( 1.58637e+00 /electron)
V_nl (planewave) : -1.1957663891e+01 ( -1.99294e+00 /electron)
V_Coul (planewave) : 3.6498602956e-01 ( 6.08310e-02 /electron)
V_xc (planewave) : -5.0877066444e+00 ( -8.47951e-01 /electron)
Viral Coefficient : -6.3115035278e-01
orbital energy:
5.4500741e-01 ( 14.831eV)
5.4500728e-01 ( 14.831eV)
3.8896747e-01 ( 10.584eV)
3.7572955e-01 ( 10.224eV)
2.3810268e-01 ( 6.479eV)
-1.0451709e-16 ( -0.000eV)
== Center of Charge ==
spin up = ( -0.0000 -0.0000 -0.0000 )
spin down = ( -0.0000 -0.0000 -0.0000 )
total = ( -0.0000 -0.0000 -0.0000 )
ionic = ( 1.4954 1.4954 1.4954 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 17.9453 17.9453 17.9453 ) au
|mu| = 31.0821 au ( 78.9982 Debye )
Ion Forces (au):
1 W ( -0.00000 0.00000 0.00000 )
2 W ( -0.00000 -0.00000 0.00000 )
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 3.265e-02
main loop : 6.849e-02
epilogue : 6.800e-04
total : 1.018e-01
cputime/step: 1.142e-03 ( 60 evaluations, 16 linesearches)
Time spent doing total step percent
total time 2.371587e-01 3.952646e-03 100.00%
total FFT time 9.016565e-02 1.502761e-03 38.02%
lagrange multipliers 1.203740e-04 2.006233e-06 0.05%
local potentials 1.235200e-05 2.058667e-07 0.01%
non-local potentials 2.684057e-03 4.473428e-05 1.13%
ffm_dgemm 8.151720e-04 1.358620e-05 0.34%
fmf_dgemm 1.364254e-03 2.273757e-05 0.58%
m_diagonalize 3.855290e-04 6.425483e-06 0.16%
mmm_multiply 9.124900e-05 1.520817e-06 0.04%
SCVtrans 7.666300e-05 1.277717e-06 0.03%
>>> job completed at Wed Feb 8 15:50:51 2023 <<<
*****************************************************
* *
* 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 Wed Feb 8 15:50:51 2023 <<<
psp_library: /home/sjplimp/nwchem/PWDFT/Nwpw/libraryps
writing formatted psp filename: ./W.vpp
generating random psi from scratch
Warning - Gram-Schmidt being performed on psi2
- exact norm = 24 norm=24.6534 corrected norm=24 (error=0.65341)
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 1
processor grid : 1 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: W valence charge = 6.0 lmax =2
comment = Troullier-Martins pseudopotential
pseudopotential type = 0
highest angular component = 2
local potential used = 0
number of non-local projections = 8
semicore corrections inlcuded = 1.800 (radius) 4.591 (charge)
cutoff = 2.389 3.185 2.244
total charge = 0.000
atom composition:
W : 4
initial ion positions (au):
1 W ( 0.00000 0.00000 0.00000 ) - atomic mass = 183.951
2 W ( 2.66457 0.00000 1.88413 ) - atomic mass = 183.951
3 W ( 2.66457 2.66457 3.76827 ) - atomic mass = 183.951
4 W ( 0.00000 2.66457 5.65240 ) - atomic mass = 183.951
G.C. ( 1.33228 1.33228 2.82620 )
C.O.M. ( 1.33228 1.33228 2.82620 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 12 ( 12 per task) down = 12 ( 12 per task)
supercell:
volume = 214.04
lattice: a1 = < 5.329 0.000 0.000 >
a2 = < 0.000 5.329 0.000 >
a3 = < 0.000 0.000 7.537 >
reciprocal: b1 = < 1.179 0.000 0.000 >
b2 = < 0.000 1.179 0.000 >
b3 = < 0.000 0.000 0.834 >
lattice: a = 5.329 b = 5.329 c = 7.537
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 10.000 fft = 10 x 10 x 12 ( 160 waves 160 per task)
wavefnc cutoff = 5.000 fft = 10 x 10 x 12 ( 62 waves 62 per task)
Ewald parameters:
energy cutoff = 10.000 fft = 10 x 10 x 12 ( 160 waves 160 per task)
Ewald summation: cut radius = 1.696 and 1
Mandelung Wigner-Seitz = 1.68382487 (alpha = 2.71431215 rs = 3.71078182)
technical parameters:
fixed step: 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 Wed Feb 8 15:50:51 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -3.263325288087e+01 -2.370052e-01 2.755915e-03
20 -3.342232241827e+01 -5.863540e-02 2.971603e-04
30 -3.391324997303e+01 -3.187197e-02 1.546984e-04
40 -3.413597312443e+01 -2.155176e-02 1.238590e-04
50 -3.438373510198e+01 -2.450980e-02 1.027256e-04
60 -3.455017548679e+01 -9.891297e-03 4.618600e-05
70 -3.464713762751e+01 -1.297081e-03 6.690651e-05
80 -3.465330146645e+01 -8.056294e-04 7.652741e-04
90 -3.466599502278e+01 -8.084057e-04 1.644931e-04
100 -3.466738274142e+01 -4.655569e-05 6.208520e-06
110 -3.466755259026e+01 -6.106702e-06 9.485566e-07
120 -3.466757480938e+01 -5.729432e-07 6.423950e-08
130 -3.466757780500e+01 -9.928726e-08 1.501512e-08
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:50:52 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 11.00000 down= 11.00000 (real space)
total energy : -3.4667577805e+01 ( -8.66689e+00 /ion)
total orbital energy: 2.4064172121e+01 ( 2.00535e+00 /electron)
hartree energy : 6.5304190697e-01 ( 5.44202e-02 /electron)
exc-corr energy : -2.0726372095e+01 ( -1.72720e+00 /electron)
ion-ion energy : -5.1462578555e+01 ( -1.28656e+01 /ion)
kinetic (planewave) : 3.2744878583e+01 ( 2.72874e+00 /electron)
V_local (planewave) : 3.5170322604e+01 ( 2.93086e+00 /electron)
V_nl (planewave) : -3.1046870249e+01 ( -2.58724e+00 /electron)
V_Coul (planewave) : 1.3060838139e+00 ( 1.08840e-01 /electron)
V_xc (planewave) : -1.4110242631e+01 ( -1.17585e+00 /electron)
Viral Coefficient : -2.6510119560e-01
orbital energy:
1.4424311e+00 ( 39.251eV)
1.2160817e+00 ( 33.092eV)
1.2090712e+00 ( 32.901eV)
1.2054584e+00 ( 32.802eV)
1.1963001e+00 ( 32.553eV)
1.1954706e+00 ( 32.531eV)
9.9977937e-01 ( 27.206eV)
9.9502181e-01 ( 27.076eV)
8.8723317e-01 ( 24.143eV)
8.8678761e-01 ( 24.131eV)
7.9845106e-01 ( 21.727eV)
4.8910438e-09 ( 0.000eV)
== Center of Charge ==
spin up = ( -0.0000 -0.0000 -0.0252 )
spin down = ( -0.0000 -0.0000 -0.0252 )
total = ( -0.0000 -0.0000 -0.0252 )
ionic = ( 1.3323 1.3323 2.8262 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 31.9757 31.9749 68.4348 ) au
|mu| = 82.0253 au ( 208.4756 Debye )
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 3.165e-02
main loop : 2.041e-01
epilogue : 2.420e-04
total : 2.360e-01
cputime/step: 4.895e-04 ( 417 evaluations, 130 linesearches)
Time spent doing total step percent
total time 4.768254e-01 1.143466e-03 100.00%
total FFT time 1.999377e-01 4.794670e-04 41.93%
lagrange multipliers 2.882320e-04 6.912038e-07 0.06%
local potentials 1.690100e-05 4.052998e-08 0.00%
non-local potentials 9.458152e-03 2.268142e-05 1.98%
ffm_dgemm 3.570522e-03 8.562403e-06 0.75%
fmf_dgemm 6.136461e-03 1.471573e-05 1.29%
m_diagonalize 1.844062e-03 4.422211e-06 0.39%
mmm_multiply 4.760850e-04 1.141691e-06 0.10%
SCVtrans 2.489650e-04 5.970384e-07 0.05%
>>> job completed at Wed Feb 8 15:50:52 2023 <<<
*****************************************************
* *
* 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 Wed Feb 8 15:50:52 2023 <<<
psp_library: /home/sjplimp/nwchem/PWDFT/Nwpw/libraryps
writing formatted psp filename: ./W.vpp
psi grids are being converted:
-----------------------------:
converting .... psi:1 spin:1
converting .... psi:2 spin:1
converting .... psi:3 spin:1
converting .... psi:4 spin:1
converting .... psi:5 spin:1
converting .... psi:6 spin:1
converting .... psi:7 spin:1
converting .... psi:8 spin:1
converting .... psi:9 spin:1
converting .... psi:10 spin:1
converting .... psi:11 spin:1
converting .... psi:12 spin:1
input psi exists, reading from file: ./nwchemex.movecs
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 1
processor grid : 1 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: W valence charge = 6.0 lmax =2
comment = Troullier-Martins pseudopotential
pseudopotential type = 0
highest angular component = 2
local potential used = 0
number of non-local projections = 8
semicore corrections inlcuded = 1.800 (radius) 4.595 (charge)
cutoff = 2.389 3.185 2.244
total charge = 0.000
atom composition:
W : 4
initial ion positions (au):
1 W ( 0.00000 0.00000 0.00000 ) - atomic mass = 183.951
2 W ( 2.66457 0.00000 1.88413 ) - atomic mass = 183.951
3 W ( 2.66457 2.66457 3.76827 ) - atomic mass = 183.951
4 W ( 0.00000 2.66457 5.65240 ) - atomic mass = 183.951
G.C. ( 1.33228 1.33228 2.82620 )
C.O.M. ( 1.33228 1.33228 2.82620 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 12 ( 12 per task) down = 12 ( 12 per task)
supercell:
volume = 214.04
lattice: a1 = < 5.329 0.000 0.000 >
a2 = < 0.000 5.329 0.000 >
a3 = < 0.000 0.000 7.537 >
reciprocal: b1 = < 1.179 0.000 0.000 >
b2 = < 0.000 1.179 0.000 >
b3 = < 0.000 0.000 0.834 >
lattice: a = 5.329 b = 5.329 c = 7.537
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 20.000 fft = 12 x 12 x 16 ( 460 waves 460 per task)
wavefnc cutoff = 10.000 fft = 12 x 12 x 16 ( 160 waves 160 per task)
Ewald parameters:
energy cutoff = 20.000 fft = 12 x 12 x 16 ( 460 waves 460 per task)
Ewald summation: cut radius = 1.696 and 1
Mandelung Wigner-Seitz = 1.68382487 (alpha = 2.71431215 rs = 3.71078182)
technical parameters:
fixed step: 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 Wed Feb 8 15:50:52 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -3.869390116272e+01 -6.903668e-05 1.222538e-06
20 -3.869394600954e+01 -2.584005e-08 7.565630e-10
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:50:52 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 11.00000 down= 11.00000 (real space)
total energy : -3.8693946010e+01 ( -9.67349e+00 /ion)
total orbital energy: 2.0571849938e+01 ( 1.71432e+00 /electron)
hartree energy : 1.0464327958e+00 ( 8.72027e-02 /electron)
exc-corr energy : -2.1151466566e+01 ( -1.76262e+00 /electron)
ion-ion energy : -5.1462581523e+01 ( -1.28656e+01 /ion)
kinetic (planewave) : 3.7980397820e+01 ( 3.16503e+00 /electron)
V_local (planewave) : 3.8936852411e+01 ( 3.24474e+00 /electron)
V_nl (planewave) : -4.4043580948e+01 ( -3.67030e+00 /electron)
V_Coul (planewave) : 2.0928655917e+00 ( 1.74405e-01 /electron)
V_xc (planewave) : -1.4394684937e+01 ( -1.19956e+00 /electron)
Viral Coefficient : -4.5835612267e-01
orbital energy:
1.2624273e+00 ( 34.353eV)
1.0588423e+00 ( 28.813eV)
1.0519217e+00 ( 28.624eV)
1.0510387e+00 ( 28.600eV)
1.0124484e+00 ( 27.550eV)
1.0116561e+00 ( 27.529eV)
7.9997475e-01 ( 21.769eV)
7.9985716e-01 ( 21.765eV)
7.5624184e-01 ( 20.579eV)
7.4126320e-01 ( 20.171eV)
7.4025353e-01 ( 20.143eV)
1.6826541e-12 ( 0.000eV)
== Center of Charge ==
spin up = ( -0.0000 -0.0000 -0.0237 )
spin down = ( -0.0000 -0.0000 -0.0237 )
total = ( -0.0000 -0.0000 -0.0237 )
ionic = ( 1.3323 1.3323 2.8262 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 31.9750 31.9748 68.3970 ) au
|mu| = 81.9935 au ( 208.3948 Debye )
Ion Forces (au):
1 W ( -0.00005 -0.00003 0.52530 )
2 W ( 0.00004 0.00003 -0.52538 )
3 W ( 0.00004 0.00002 0.52530 )
4 W ( -0.00005 -0.00002 -0.52538 )
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 3.828e-02
main loop : 6.028e-02
epilogue : 7.240e-04
total : 9.929e-02
cputime/step: 8.998e-04 ( 67 evaluations, 18 linesearches)
Time spent doing total step percent
total time 5.763748e-01 8.602609e-03 100.00%
total FFT time 2.314689e-01 3.454759e-03 40.16%
lagrange multipliers 5.522480e-04 8.242507e-06 0.10%
local potentials 3.313000e-05 4.944776e-07 0.01%
non-local potentials 1.250012e-02 1.865689e-04 2.17%
ffm_dgemm 4.586577e-03 6.845637e-05 0.80%
fmf_dgemm 7.988636e-03 1.192334e-04 1.39%
m_diagonalize 2.089830e-03 3.119149e-05 0.36%
mmm_multiply 5.259960e-04 7.850687e-06 0.09%
SCVtrans 2.736630e-04 4.084522e-06 0.05%
>>> job completed at Wed Feb 8 15:50:52 2023 <<<

66
examples/QUANTUM/NWChem/log.8Feb23.series.w.bcc.1 Normal file
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@ -0,0 +1,66 @@
read_data data.${datafile}
read_data data.w.bcc
Reading data file ...
orthogonal box = (0 0 0) to (3.1654062 3.1654062 3.1654062)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
read_data CPU = 0.000 seconds
mass 1 183.84
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm elements W connect no
fix_modify 1 energy yes
#dump 1 all custom 1 dump.series.${datafile}.$p id x y z fx fy fz
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
Per MPI rank memory allocation (min/avg/max) = 2.301 | 2.301 | 2.301 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 -577.92971 2.3538612e-305
Loop time of 5.01e-07 on 1 procs for 0 steps with 2 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 5.01e-07 | | |100.00
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 33 ave 33 max 33 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
clear
next datafile
jump SELF loop
units metal
atom_style atomic
atom_modify map yes
comm_modify cutoff 2.0
log log.series.${datafile}.$p
log log.series.w.diamond.$p
log log.series.w.diamond.1

60
examples/QUANTUM/NWChem/log.8Feb23.series.w.diamond.1 Normal file
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@ -0,0 +1,60 @@
read_data data.${datafile}
read_data data.w.diamond
Reading data file ...
orthogonal box = (0 0 0) to (2.8200564 2.8200564 3.988162)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
read_data CPU = 0.000 seconds
mass 1 183.84
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm elements W connect no
fix_modify 1 energy yes
#dump 1 all custom 1 dump.series.${datafile}.$p id x y z fx fy fz
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
Per MPI rank memory allocation (min/avg/max) = 2.301 | 2.301 | 2.301 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 -1052.9159 2.3538612e-305
Loop time of 6.97e-07 on 1 procs for 0 steps with 4 atoms
143.5% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 6.97e-07 | | |100.00
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 55 ave 55 max 55 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
clear
next datafile
jump SELF loop
mdi exit
Total wall time: 0:00:00

1196
examples/QUANTUM/NWChem/log.8Feb23.water.pwdft.qmmm.mpi.2 Normal file
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File diff suppressed because it is too large Load Diff

954
examples/QUANTUM/NWChem/log.8Feb23.water.pwdft.qmmm.plugin.2 Normal file
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@ -0,0 +1,954 @@
*****************************************************
* *
* 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 Wed Feb 8 15:51:08 2023 <<<
psp_library: /home/sjplimp/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
- not self-consistent
writing formatted psp filename: ./O.vpp
writing formatted psp filename: ./H.vpp
generating random psi from scratch
Warning - Gram-Schmidt being performed on psi2
- exact norm = 8.00000 norm=8.86148 corrected norm=8.00000 (error=0.86148)
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 2
processor grid : 2 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 ( 0.30530 -0.09999 0.06269 ) - atomic mass = 15.995
2 H ( 1.51755 0.69756 -0.96690 ) - atomic mass = 1.008
3 H ( -0.61524 -1.26531 -0.92324 ) - atomic mass = 1.008
G.C. ( 0.40254 -0.22258 -0.60915 )
C.O.M. ( 0.32163 -0.12057 -0.05011 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 4 ( 4 per task) down = 4 ( 4 per task)
supercell:
volume = 17575.98
lattice: a1 = < 26.000 0.000 0.000 >
a2 = < 0.000 26.000 0.000 >
a3 = < 0.000 0.000 26.000 >
reciprocal: b1 = < 0.242 0.000 0.000 >
b2 = < 0.000 0.242 0.000 >
b3 = < 0.000 0.000 0.242 >
lattice: a = 26.000 b = 26.000 c = 26.000
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 20.000 fft = 54 x 54 x 54 ( 37447 waves 18724 per task)
wavefnc cutoff = 10.000 fft = 54 x 54 x 54 ( 13373 waves 6687 per task)
Ewald parameters:
energy cutoff = 20.000 fft = 54 x 54 x 54 ( 37447 waves 18724 per task)
Ewald summation: cut radius = 8.276 and 1
Mandelung Wigner-Seitz = 1.76011888 (alpha = 2.83729748 rs = 16.12910517)
technical parameters:
fixed step: time step = 5.80 ficticious mass = 400000.00
tolerance = 1.000e-09 (energy) 1.000e+00 (density) 1.000e-04 (ion)
max iterations = 1000 ( 10 inner 100 outer)
minimizer = Grassmann conjugate gradient
============ Grassmann conjugate gradient iteration ============
>>> iteration started at Wed Feb 8 15:51:09 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -1.206279801672e+01 -4.150120e-01 1.996397e-03
20 -1.493506122443e+01 -1.422834e-01 1.506682e-03
30 -1.540348600009e+01 -2.354360e-02 7.931449e-05
40 -1.566981091704e+01 -3.162288e-02 2.353093e-04
50 -1.598278441045e+01 -2.666532e-02 2.366148e-04
60 -1.616463354121e+01 -1.223350e-02 7.334903e-05
70 -1.630473193885e+01 -3.266566e-04 2.297099e-06
80 -1.630526899088e+01 -2.459563e-06 7.181128e-09
90 -1.630527200045e+01 -1.255258e-08 3.774166e-10
100 -1.630527202340e+01 -8.822809e-10 1.152800e-11
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:51:18 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 4.00000 down= 4.00000 (real space)
total energy : -1.6305272023e+01 ( -5.43509e+00 /ion)
total orbital energy: -4.4098310387e+00 ( -1.10246e+00 /electron)
hartree energy : 1.6681756106e+01 ( 4.17044e+00 /electron)
exc-corr energy : -4.0100672760e+00 ( -1.00252e+00 /electron)
ion-ion energy : 3.5966388474e+00 ( 1.19888e+00 /ion)
kinetic (planewave) : 9.8614028188e+00 ( 2.46535e+00 /electron)
V_local (planewave) : -4.2645184847e+01 ( -1.06613e+01 /electron)
V_nl (planewave) : 2.1018232722e-01 ( 5.25456e-02 /electron)
V_Coul (planewave) : 3.3363512212e+01 ( 8.34088e+00 /electron)
V_xc (planewave) : -5.1997435500e+00 ( -1.29994e+00 /electron)
Viral Coefficient : -1.4471809052e+00
orbital energy:
-2.5265267e-01 ( -6.875eV)
-3.5266167e-01 ( -9.596eV)
-5.0407048e-01 ( -13.717eV)
-1.0955307e+00 ( -29.811eV)
== Center of Charge ==
spin up = ( 0.3337 -0.1357 -0.1342 )
spin down = ( 0.3337 -0.1357 -0.1342 )
total = ( 0.3337 -0.1357 -0.1342 )
ionic = ( 0.3418 -0.1460 -0.1893 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 0.0648 -0.0818 -0.4407 ) au
|mu| = 0.4529 au ( 1.1511 Debye )
*************************************************************
** **
** 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
- not self-consistent
charge analysis on each atom
----------------------------
no atom Qelc Qion Qtotal
----- ---- ------- ------- -------
1 O -6.416 6.000 -0.416
2 H -0.792 1.000 0.208
3 H -0.792 1.000 0.208
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 -0.083 -2.968 -3.365
2 H 1.000 -0.973 1.287 -1.106
3 H 1.000 -0.969 1.282 -1.104
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 1.158e-01
main loop : 9.264e+00
epilogue : 8.508e-03
total : 9.388e+00
cputime/step: 2.932e-02 ( 316 evaluations, 97 linesearches)
Time spent doing total step percent
total time 9.361045e+00 2.962356e-02 100.00%
total FFT time 4.391524e+00 1.389723e-02 46.91%
lagrange multipliers 1.000841e-03 3.167218e-06 0.01%
local potentials 4.544660e-04 1.438184e-06 0.00%
non-local potentials 2.664875e-01 8.433148e-04 2.85%
ffm_dgemm 4.429686e-02 1.401799e-04 0.47%
fmf_dgemm 9.898879e-02 3.132557e-04 1.06%
m_diagonalize 6.658380e-04 2.107082e-06 0.01%
mmm_multiply 1.051730e-04 3.328259e-07 0.00%
SCVtrans 2.827170e-04 8.946741e-07 0.00%
>>> job completed at Wed Feb 8 15:51:18 2023 <<<
*****************************************************
* *
* 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 Wed Feb 8 15:51:18 2023 <<<
psp_library: /home/sjplimp/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
- not self-consistent
writing formatted psp filename: ./O.vpp
writing formatted psp filename: ./H.vpp
psi grids are being converted:
-----------------------------:
converting .... psi:1 spin:1
converting .... psi:2 spin:1
converting .... psi:3 spin:1
converting .... psi:4 spin:1
input psi exists, reading from file: ./nwchemex.movecs
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 2
processor grid : 2 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 ( 0.30530 -0.09999 0.06269 ) - atomic mass = 15.995
2 H ( 1.51755 0.69756 -0.96690 ) - atomic mass = 1.008
3 H ( -0.61524 -1.26531 -0.92324 ) - atomic mass = 1.008
G.C. ( 0.40254 -0.22258 -0.60915 )
C.O.M. ( 0.32163 -0.12057 -0.05011 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 4 ( 4 per task) down = 4 ( 4 per task)
supercell:
volume = 17575.98
lattice: a1 = < 26.000 0.000 0.000 >
a2 = < 0.000 26.000 0.000 >
a3 = < 0.000 0.000 26.000 >
reciprocal: b1 = < 0.242 0.000 0.000 >
b2 = < 0.000 0.242 0.000 >
b3 = < 0.000 0.000 0.242 >
lattice: a = 26.000 b = 26.000 c = 26.000
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 40.000 fft = 80 x 80 x 80 ( 106048 waves 53024 per task)
wavefnc cutoff = 20.000 fft = 80 x 80 x 80 ( 37447 waves 18724 per task)
Ewald parameters:
energy cutoff = 40.000 fft = 80 x 80 x 80 ( 106048 waves 53024 per task)
Ewald summation: cut radius = 8.276 and 1
Mandelung Wigner-Seitz = 1.76011888 (alpha = 2.83729748 rs = 16.12910517)
technical parameters:
fixed step: time step = 5.80 ficticious mass = 400000.00
tolerance = 1.000e-09 (energy) 1.000e+00 (density) 1.000e-04 (ion)
max iterations = 1000 ( 10 inner 100 outer)
minimizer = Grassmann conjugate gradient
============ Grassmann conjugate gradient iteration ============
>>> iteration started at Wed Feb 8 15:51:18 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -1.709563334317e+01 -6.201449e-04 4.252710e-06
20 -1.709727702922e+01 -1.395575e-05 2.324062e-07
30 -1.709728935247e+01 -1.652084e-07 9.382706e-10
40 -1.709728957157e+01 -1.886704e-09 1.155902e-11
50 -1.709728957460e+01 -8.623040e-10 2.854954e-12
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:51:33 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 4.00000 down= 4.00000 (real space)
total energy : -1.7097289575e+01 ( -5.69910e+00 /ion)
total orbital energy: -4.0996983104e+00 ( -1.02492e+00 /electron)
hartree energy : 1.7847984194e+01 ( 4.46200e+00 /electron)
exc-corr energy : -4.2204936652e+00 ( -1.05512e+00 /electron)
ion-ion energy : 3.5966388474e+00 ( 1.19888e+00 /ion)
kinetic (planewave) : 1.2079256812e+01 ( 3.01981e+00 /electron)
V_local (planewave) : -4.5359046100e+01 ( -1.13398e+01 /electron)
V_nl (planewave) : -1.0416296625e+00 ( -2.60407e-01 /electron)
V_Coul (planewave) : 3.5695968387e+01 ( 8.92399e+00 /electron)
V_xc (planewave) : -5.4742477473e+00 ( -1.36856e+00 /electron)
Viral Coefficient : -1.3393998798e+00
orbital energy:
-2.6700298e-01 ( -7.266eV)
-3.3720536e-01 ( -9.176eV)
-5.0189171e-01 ( -13.657eV)
-9.4374911e-01 ( -25.681eV)
== Center of Charge ==
spin up = ( 0.3298 -0.1310 -0.1068 )
spin down = ( 0.3298 -0.1310 -0.1068 )
total = ( 0.3298 -0.1310 -0.1068 )
ionic = ( 0.3418 -0.1460 -0.1893 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 0.0958 -0.1200 -0.6599 ) au
|mu| = 0.6776 au ( 1.7221 Debye )
*************************************************************
** **
** 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
- not self-consistent
charge analysis on each atom
----------------------------
no atom Qelc Qion Qtotal
----- ---- ------- ------- -------
1 O -6.631 6.000 -0.631
2 H -0.684 1.000 0.316
3 H -0.685 1.000 0.315
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 -0.775 -2.618 -3.238
2 H 1.000 -0.768 0.898 -0.814
3 H 1.000 -0.766 0.895 -0.814
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 1.750e-01
main loop : 1.525e+01
epilogue : 2.840e-02
total : 1.546e+01
cputime/step: 1.038e-01 ( 147 evaluations, 43 linesearches)
Time spent doing total step percent
total time 2.486473e+01 1.691478e-01 100.00%
total FFT time 1.180442e+01 8.030220e-02 47.47%
lagrange multipliers 5.373788e-03 3.655638e-05 0.02%
local potentials 1.815201e-03 1.234831e-05 0.01%
non-local potentials 6.301919e-01 4.287020e-03 2.53%
ffm_dgemm 1.205239e-01 8.198904e-04 0.48%
fmf_dgemm 2.346519e-01 1.596271e-03 0.94%
m_diagonalize 9.745520e-04 6.629605e-06 0.00%
mmm_multiply 1.509190e-04 1.026660e-06 0.00%
SCVtrans 4.188950e-04 2.849626e-06 0.00%
>>> job completed at Wed Feb 8 15:51:33 2023 <<<
*****************************************************
* *
* 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 Wed Feb 8 15:51:33 2023 <<<
psp_library: /home/sjplimp/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 0.03217
APC u: 2 0.01847
APC u: 3 0.01917
- self-consistent
writing formatted psp filename: ./O.vpp
writing formatted psp filename: ./H.vpp
psi grids are being converted:
-----------------------------:
converting .... psi:1 spin:1
converting .... psi:2 spin:1
converting .... psi:3 spin:1
converting .... psi:4 spin:1
input psi exists, reading from file: ./nwchemex.movecs
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 2
processor grid : 2 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 ( 0.30530 -0.09999 0.06269 ) - atomic mass = 15.995
2 H ( 1.51755 0.69756 -0.96690 ) - atomic mass = 1.008
3 H ( -0.61524 -1.26531 -0.92324 ) - atomic mass = 1.008
G.C. ( 0.40254 -0.22258 -0.60915 )
C.O.M. ( 0.32163 -0.12057 -0.05011 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 4 ( 4 per task) down = 4 ( 4 per task)
supercell:
volume = 17575.98
lattice: a1 = < 26.000 0.000 0.000 >
a2 = < 0.000 26.000 0.000 >
a3 = < 0.000 0.000 26.000 >
reciprocal: b1 = < 0.242 0.000 0.000 >
b2 = < 0.000 0.242 0.000 >
b3 = < 0.000 0.000 0.242 >
lattice: a = 26.000 b = 26.000 c = 26.000
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 60.000 fft = 96 x 96 x 96 ( 195216 waves 97608 per task)
wavefnc cutoff = 30.000 fft = 96 x 96 x 96 ( 69013 waves 34507 per task)
Ewald parameters:
energy cutoff = 60.000 fft = 96 x 96 x 96 ( 195216 waves 97608 per task)
Ewald summation: cut radius = 8.276 and 1
Mandelung Wigner-Seitz = 1.76011888 (alpha = 2.83729748 rs = 16.12910517)
technical parameters:
fixed step: time step = 5.80 ficticious mass = 400000.00
tolerance = 1.000e-09 (energy) 1.000e+00 (density) 1.000e-04 (ion)
max iterations = 1000 ( 10 inner 100 outer)
minimizer = Grassmann conjugate gradient
============ Grassmann conjugate gradient iteration ============
>>> iteration started at Wed Feb 8 15:51:34 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
- 10 steepest descent iterations performed
10 -1.719854750853e+01 -5.739066e-05 1.086836e-06
20 -1.719866697103e+01 -1.561353e-06 7.029039e-08
30 -1.719867013369e+01 -4.633685e-08 1.534758e-10
40 -1.719867027116e+01 -2.335167e-09 4.231098e-11
50 -1.719867027638e+01 -8.363159e-10 1.415691e-11
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:52:07 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 4.00000 down= 4.00000 (real space)
APC Potential:
0.032168321 0.018471985 0.019170642
APC Point Charges:
-0.742599484 0.372218634 0.370380850
total energy : -1.7198670276e+01 ( -5.73289e+00 /ion)
total orbital energy: -4.1186005526e+00 ( -1.02965e+00 /electron)
hartree energy : 1.8012763373e+01 ( 4.50319e+00 /electron)
exc-corr energy : -4.2447731088e+00 ( -1.06119e+00 /electron)
APC energy : -9.9121231907e-03 ( -3.30404e-03 /ion)
ion-ion energy : 3.5966383352e+00 ( 1.19888e+00 /ion)
kinetic (planewave) : 1.2411600602e+01 ( 3.10290e+00 /electron)
V_local (planewave) : -4.5793468974e+01 ( -1.14484e+01 /electron)
V_nl (planewave) : -1.2574819137e+00 ( -3.14370e-01 /electron)
V_Coul (planewave) : 3.6025526746e+01 ( 9.00638e+00 /electron)
V_xc (planewave) : -5.5047770128e+00 ( -1.37619e+00 /electron)
K.S. V_APC energy : -8.5963533405e-02 ( -2.86545e-02 /ion)
Viral Coefficient : -1.3318347637e+00
orbital energy:
-2.7467794e-01 ( -7.474eV)
-3.4392861e-01 ( -9.359eV)
-5.0664632e-01 ( -13.787eV)
-9.3404742e-01 ( -25.417eV)
== Center of Charge ==
spin up = ( 0.3274 -0.1283 -0.0913 )
spin down = ( 0.3274 -0.1283 -0.0913 )
total = ( 0.3274 -0.1283 -0.0913 )
ionic = ( 0.3418 -0.1460 -0.1893 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 0.1153 -0.1410 -0.7838 ) au
|mu| = 0.8046 au ( 2.0451 Debye )
Ion Forces (au):
1 O ( 0.00014 -0.00159 0.00561 )
2 H ( -0.00082 -0.00158 -0.00230 )
3 H ( 0.00231 0.00170 -0.00152 )
*************************************************************
** **
** 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:
0.032168321 0.018471985 0.019170642
APC Point Charges:
-0.742599484 0.372218634 0.370380850
charge analysis on each atom
----------------------------
no atom Qelc Qion Qtotal
----- ---- ------- ------- -------
1 O -6.743 6.000 -0.743
2 H -0.628 1.000 0.372
3 H -0.630 1.000 0.370
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 -1.097 -2.076 -3.569
2 H 1.000 -0.718 0.776 -0.685
3 H 1.000 -0.718 0.778 -0.690
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 2.776e-01
main loop : 3.341e+01
epilogue : 8.123e-02
total : 3.377e+01
cputime/step: 2.258e-01 ( 148 evaluations, 44 linesearches)
Time spent doing total step percent
total time 5.870426e+01 3.966504e-01 100.00%
total FFT time 2.757222e+01 1.862988e-01 46.97%
lagrange multipliers 1.439599e-02 9.727022e-05 0.02%
local potentials 2.612066e-01 1.764910e-03 0.44%
non-local potentials 1.313983e+00 8.878267e-03 2.24%
ffm_dgemm 2.830021e-01 1.912177e-03 0.48%
fmf_dgemm 5.364307e-01 3.624532e-03 0.91%
m_diagonalize 1.321422e-03 8.928527e-06 0.00%
mmm_multiply 2.068650e-04 1.397736e-06 0.00%
SCVtrans 6.028430e-04 4.073264e-06 0.00%
>>> job completed at Wed Feb 8 15:52:07 2023 <<<
*****************************************************
* *
* 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 Wed Feb 8 15:52:07 2023 <<<
psp_library: /home/sjplimp/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 0.03217
APC u: 2 0.01848
APC u: 3 0.01917
- self-consistent
reading formatted psp filename: ./O.vpp
reading formatted psp filename: ./H.vpp
input psi exists, reading from file: ./nwchemex.movecs
============== summary of input ==================
input psi filename: ./nwchemex.movecs
number of processors used: 2
processor grid : 2 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 ( 0.30530 -0.09999 0.06269 ) - atomic mass = 15.995
2 H ( 1.51755 0.69755 -0.96692 ) - atomic mass = 1.008
3 H ( -0.61523 -1.26531 -0.92326 ) - atomic mass = 1.008
G.C. ( 0.40254 -0.22258 -0.60916 )
C.O.M. ( 0.32163 -0.12057 -0.05011 )
real space Electric field:
Electric Field (au) = ( 0.00000 0.00000 0.00000 )
Center (au) = ( 0.00000 0.00000 0.00000 )
number of electrons: spin up = 4 ( 4 per task) down = 4 ( 4 per task)
supercell:
volume = 17575.98
lattice: a1 = < 26.000 0.000 0.000 >
a2 = < 0.000 26.000 0.000 >
a3 = < 0.000 0.000 26.000 >
reciprocal: b1 = < 0.242 0.000 0.000 >
b2 = < 0.000 0.242 0.000 >
b3 = < 0.000 0.000 0.242 >
lattice: a = 26.000 b = 26.000 c = 26.000
alpha = 90.000 beta = 90.000 gamma = 90.000
density cutoff = 60.000 fft = 96 x 96 x 96 ( 195216 waves 97608 per task)
wavefnc cutoff = 30.000 fft = 96 x 96 x 96 ( 69013 waves 34507 per task)
Ewald parameters:
energy cutoff = 60.000 fft = 96 x 96 x 96 ( 195216 waves 97608 per task)
Ewald summation: cut radius = 8.276 and 1
Mandelung Wigner-Seitz = 1.76011888 (alpha = 2.83729748 rs = 16.12910517)
technical parameters:
fixed step: time step = 5.80 ficticious mass = 400000.00
tolerance = 1.000e-09 (energy) 1.000e+00 (density) 1.000e-04 (ion)
max iterations = 1000 ( 10 inner 100 outer)
minimizer = Grassmann conjugate gradient
============ Grassmann conjugate gradient iteration ============
>>> iteration started at Wed Feb 8 15:52:07 2023 <<<
iter. Energy DeltaE DeltaRho
----------------------------------------------------------------
10 -1.719867286753e+01 -6.805578e-10 2.321480e-11
*** tolerance ok. iteration terminated
>>> iteration ended at Wed Feb 8 15:52:08 2023 <<<
============== energy results (Molecule object) ==============
number of electrons: spin up= 4.00000 down= 4.00000 (real space)
APC Potential:
0.032174976 0.018475289 0.019174010
APC Point Charges:
-0.742603988 0.372221498 0.370382490
total energy : -1.7198672868e+01 ( -5.73289e+00 /ion)
total orbital energy: -4.1185877729e+00 ( -1.02965e+00 /electron)
hartree energy : 1.8012764978e+01 ( 4.50319e+00 /electron)
exc-corr energy : -4.2447737993e+00 ( -1.06119e+00 /electron)
APC energy : -9.9146481390e-03 ( -3.30488e-03 /ion)
ion-ion energy : 3.5966070435e+00 ( 1.19887e+00 /ion)
kinetic (planewave) : 1.2411604235e+01 ( 3.10290e+00 /electron)
V_local (planewave) : -4.5793466800e+01 ( -1.14484e+01 /electron)
V_nl (planewave) : -1.2574773463e+00 ( -3.14369e-01 /electron)
V_Coul (planewave) : 3.6025529957e+01 ( 9.00638e+00 /electron)
V_xc (planewave) : -5.5047778182e+00 ( -1.37619e+00 /electron)
K.S. V_APC energy : -8.5983469376e-02 ( -2.86612e-02 /ion)
Viral Coefficient : -1.3318336369e+00
orbital energy:
-2.7467727e-01 ( -7.474eV)
-3.4393166e-01 ( -9.359eV)
-5.0664047e-01 ( -13.786eV)
-9.3404449e-01 ( -25.417eV)
== Center of Charge ==
spin up = ( 0.3274 -0.1283 -0.0913 )
spin down = ( 0.3274 -0.1283 -0.0913 )
total = ( 0.3274 -0.1283 -0.0913 )
ionic = ( 0.3418 -0.1460 -0.1893 )
== Molecular Dipole wrt Center of Mass ==
mu = ( 0.1153 -0.1410 -0.7838 ) au
|mu| = 0.8047 au ( 2.0451 Debye )
Ion Forces (au):
1 O ( 0.00016 -0.00158 0.00552 )
2 H ( -0.00083 -0.00158 -0.00229 )
3 H ( 0.00230 0.00170 -0.00151 )
*************************************************************
** **
** 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:
0.032174976 0.018475289 0.019174010
APC Point Charges:
-0.742603988 0.372221498 0.370382490
charge analysis on each atom
----------------------------
no atom Qelc Qion Qtotal
----- ---- ------- ------- -------
1 O -6.743 6.000 -0.743
2 H -0.628 1.000 0.372
3 H -0.630 1.000 0.370
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 -1.098 -2.076 -3.570
2 H 1.000 -0.718 0.776 -0.685
3 H 1.000 -0.718 0.778 -0.689
output psi to filename: ./nwchemex.movecs
-----------------
cputime in seconds
prologue : 1.915e-01
main loop : 9.137e-01
epilogue : 8.119e-02
total : 1.186e+00
cputime/step: 2.284e-01 ( 4 evaluations, 1 linesearches)
Time spent doing total step percent
total time 5.992501e+01 1.498125e+01 100.00%
total FFT time 2.799652e+01 6.999131e+00 46.72%
lagrange multipliers 1.439599e-02 3.598998e-03 0.02%
local potentials 2.731576e-01 6.828941e-02 0.46%
non-local potentials 1.343674e+00 3.359185e-01 2.24%
ffm_dgemm 2.875073e-01 7.187682e-02 0.48%
fmf_dgemm 5.430685e-01 1.357671e-01 0.91%
m_diagonalize 1.342049e-03 3.355122e-04 0.00%
mmm_multiply 2.087340e-04 5.218350e-05 0.00%
SCVtrans 6.080600e-04 1.520150e-04 0.00%
>>> job completed at Wed Feb 8 15:52:08 2023 <<<

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LAMMPS (22 Dec 2022)
# QMMM with NWChem
units real
atom_style full
bond_style harmonic
angle_style harmonic
read_data data.water.qmmm
Reading data file ...
orthogonal box = (-6.879301 -6.879301 -6.879301) to (6.879301 6.879301 6.879301)
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 = 0.002 seconds
# QM atoms are 1st water
# MM atoms are 2nd water
group qm molecule 1
3 atoms in group qm
group mm molecule 2
3 atoms in group mm
# remove bonds/angles between QM atoms
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
# must specify mixing explicitly b/c hybrid/overlay
# QM O,H = types 1,2
# MM O,H = types 3,4
# QM O,H atoms do not LJ interact with each other
# only MM O atoms LJ interact with other b/c MM H is zero
# MM/QM O do LJ interact with each other, same as pair of MM O atoms
# MM O and QM H do LJ interact with each other with non-zero H epsilon = 0.044
# geometric mixing for epsilon, arithmetic for sigma
# this is to provide stability for QM H atoms
# mixing only for MM-O/QM-O and MM-O/QM-H
pair_style hybrid/overlay lj/cut 6.0 coul/cut 6.0
pair_coeff 1 1 lj/cut 0.0 3.165558
pair_coeff 2 2 lj/cut 0.0 0.7
pair_coeff 3 3 lj/cut 0.155394 3.165558
pair_coeff 4 4 lj/cut 0.0 0.7
pair_coeff 1 3 lj/cut 0.155394 3.165558
pair_coeff 2 3 lj/cut 0.08268818537130924 1.932779
pair_coeff * * coul/cut
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
# QMMM dynamics
timestep 0.1
fix 1 all nve
fix 2 qm mdi/qmmm potential elements O H O H
fix_modify 2 energy yes
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong f_2 pe etotal press
thermo 1
run 2
Generated 0 of 6 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 = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 2 0 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
Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press
0 0 0 0 0.95937448 -170.68735 -169.72797 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
1 1.3827511 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
2 4.3658207 4.6633575 0.069502914 0.95924532 -170.70698 -169.74773 3.3333254 0 -10627.871 -10794.286 -10794.216 -383.31463
Loop time of 4.36586 on 1 procs for 2 steps with 6 atoms
Performance: 0.004 ns/day, 6063.691 hours/ns, 0.458 timesteps/s, 2.749 atom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.572e-06 | 7.572e-06 | 7.572e-06 | 0.0 | 0.00
Bond | 5.119e-06 | 5.119e-06 | 5.119e-06 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.881e-06 | 2.881e-06 | 2.881e-06 | 0.0 | 0.00
Output | 5.439e-05 | 5.439e-05 | 5.439e-05 | 0.0 | 0.00
Modify | 4.3658 | 4.3658 | 4.3658 | 0.0 |100.00
Other | | 6.093e-06 | | | 0.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56 ave 56 max 56 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12
Ave neighs/atom = 2
Ave special neighs/atom = 1
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:11

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LAMMPS (22 Dec 2022)
# QMMM with NWChem
units real
atom_style full
bond_style harmonic
angle_style harmonic
read_data data.water.qmmm
Reading data file ...
orthogonal box = (-6.879301 -6.879301 -6.879301) to (6.879301 6.879301 6.879301)
1 by 1 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 = 0.000 seconds
read_data CPU = 0.003 seconds
# QM atoms are 1st water
# MM atoms are 2nd water
group qm molecule 1
3 atoms in group qm
group mm molecule 2
3 atoms in group mm
# remove bonds/angles between QM atoms
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
# must specify mixing explicitly b/c hybrid/overlay
# QM O,H = types 1,2
# MM O,H = types 3,4
# QM O,H atoms do not LJ interact with each other
# only MM O atoms LJ interact with other b/c MM H is zero
# MM/QM O do LJ interact with each other, same as pair of MM O atoms
# MM O and QM H do LJ interact with each other with non-zero H epsilon = 0.044
# geometric mixing for epsilon, arithmetic for sigma
# this is to provide stability for QM H atoms
# mixing only for MM-O/QM-O and MM-O/QM-H
pair_style hybrid/overlay lj/cut 6.0 coul/cut 6.0
pair_coeff 1 1 lj/cut 0.0 3.165558
pair_coeff 2 2 lj/cut 0.0 0.7
pair_coeff 3 3 lj/cut 0.155394 3.165558
pair_coeff 4 4 lj/cut 0.0 0.7
pair_coeff 1 3 lj/cut 0.155394 3.165558
pair_coeff 2 3 lj/cut 0.08268818537130924 1.932779
pair_coeff * * coul/cut
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
# QMMM dynamics
timestep 0.1
fix 1 all nve
fix 2 qm mdi/qmmm potential elements O H O H
fix_modify 2 energy yes
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong f_2 pe etotal press
thermo 1
variable p equal extract_setting(world_size)
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" extra "template.water.nw water.dimer.nw log.water.pwdft.qmmm.plugin.$p" command "run 1"
run 1
Generated 0 of 6 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 = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 2 0 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
Per MPI rank memory allocation (min/avg/max) = 7.453 | 7.453 | 7.453 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press
0 0 0 0 0.95937448 -170.68735 -169.72797 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
1 1.2206038 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
Loop time of 1.22062 on 2 procs for 1 steps with 6 atoms
Performance: 0.007 ns/day, 3390.614 hours/ns, 0.819 timesteps/s, 4.916 atom-step/s
88.7% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.563e-06 | 4.9165e-06 | 5.27e-06 | 0.0 | 0.00
Bond | 1.201e-06 | 2.0745e-06 | 2.948e-06 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.511e-06 | 8.0675e-06 | 8.624e-06 | 0.0 | 0.00
Output | 1.7987e-05 | 1.9748e-05 | 2.151e-05 | 0.0 | 0.00
Modify | 1.2206 | 1.2206 | 1.2206 | 0.0 |100.00
Other | | 7.148e-06 | | | 0.00
Nlocal: 3 ave 4 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 42 ave 46 max 38 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 6 ave 9 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 12
Ave neighs/atom = 2
Ave special neighs/atom = 1
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:00

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@ -0,0 +1,166 @@
LAMMPS (22 Dec 2022)
# QMMM for SiO2 zeolite with one methane molecule
units metal
atom_style full
bond_style harmonic
angle_style harmonic
read_data data.zeolite
Reading data file ...
orthogonal box = (-5.9266 -5.9266 -5.9266) to (5.9926 5.9926 5.9926)
1 by 1 by 1 MPI processor grid
reading atoms ...
77 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# MM atoms are Si,O
# QM atoms are C,H
group mm type 1 2
72 atoms in group mm
group qm type 3 4
5 atoms in group qm
# pair style must define stand-alone short-range Coulombics
# must specify mixing explicitly b/c hybrid/overlay
# MM Si,O = types 1,2
# QM C,H = types 3,4
# MM Si,O atoms do not LJ interact with each other (just via Buckingham)
# QM C,H atoms do not LJ interact with each other
# MM Si,O and QM C,H do LJ interact with each other
pair_style hybrid/overlay buck 6.5 lj/cut 6.5 coul/cut 6.5
pair_coeff 1 1 buck 3150.462646 0.35032282 626.7519553
pair_coeff 2 2 buck 659.595398 0.38609055 26.836679
pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
pair_coeff 1 3 lj/cut 0.09087 3.613
pair_coeff 1 4 lj/cut 0.0344258 3.238
pair_coeff 2 3 lj/cut 0.1419429 3.1
pair_coeff 2 4 lj/cut 0.035857762359063315 1.932779
pair_coeff 3 3 lj/cut 0.0 3.4
pair_coeff 4 4 lj/cut 0.0 2.65
pair_coeff * * coul/cut
bond_style harmonic
bond_coeff 1 29.40 1.09
angle_style harmonic
angle_coeff 1 0.172325 109.5
# remove bonds/angles in QM methane molecule
delete_bonds qm multi remove special
System init for delete_bonds ...
Generated 0 of 6 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 = 8.5
ghost atom cutoff = 8.5
binsize = 4.25, bins = 3 3 3
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair buck, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Deleting bonds ...
0 total bonds, 0 turned on, 0 turned off
0 total angles, 0 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
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.000 seconds
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
velocity all create 300.0 458732
# QMMM dynamics with small timestep
# dynamic or frozen zeolite
#fix 1 all nve
fix 1 qm nve
fix 2 qm mdi/qmmm potential elements Si O C H
fix_modify 2 energy yes
timestep 0.0001
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong f_2 pe etotal press
thermo 1
run 2
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.773 | 9.773 | 9.773 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press
0 0 300 2.9471313 -106.25003 -1065.0377 -1171.2878 0 0 -198.98094 -1370.2687 -1367.3216 -636.94701
1 10.047862 299.91218 2.9462686 -106.24961 -1065.1058 -1171.3554 0 0 -198.90989 -1370.2653 -1367.3191 -659.48199
2 21.795158 299.81521 2.945316 -106.24919 -1065.1818 -1171.431 0 0 -198.83143 -1370.2624 -1367.3171 -684.54098
Loop time of 21.7952 on 1 procs for 2 steps with 77 atoms
Performance: 0.001 ns/day, 30271.086 hours/ns, 0.092 timesteps/s, 7.066 atom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00029526 | 0.00029526 | 0.00029526 | 0.0 | 0.00
Bond | 3.746e-06 | 3.746e-06 | 3.746e-06 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3152e-05 | 1.3152e-05 | 1.3152e-05 | 0.0 | 0.00
Output | 5.9651e-05 | 5.9651e-05 | 5.9651e-05 | 0.0 | 0.00
Modify | 21.795 | 21.795 | 21.795 | 0.0 |100.00
Other | | 1.083e-05 | | | 0.00
Nlocal: 77 ave 77 max 77 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1066 ave 1066 max 1066 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3146 ave 3146 max 3146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3146
Ave neighs/atom = 40.857143
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:51

169
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@ -0,0 +1,169 @@
LAMMPS (22 Dec 2022)
# QMMM for SiO2 zeolite with one methane molecule
units metal
atom_style full
bond_style harmonic
angle_style harmonic
read_data data.zeolite
Reading data file ...
orthogonal box = (-5.9266 -5.9266 -5.9266) to (5.9926 5.9926 5.9926)
2 by 2 by 2 MPI processor grid
reading atoms ...
77 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
# MM atoms are Si,O
# QM atoms are C,H
group mm type 1 2
72 atoms in group mm
group qm type 3 4
5 atoms in group qm
# pair style must define stand-alone short-range Coulombics
# must specify mixing explicitly b/c hybrid/overlay
# MM Si,O = types 1,2
# QM C,H = types 3,4
# MM Si,O atoms do not LJ interact with each other (just via Buckingham)
# QM C,H atoms do not LJ interact with each other
# MM Si,O and QM C,H do LJ interact with each other
pair_style hybrid/overlay buck 6.5 lj/cut 6.5 coul/cut 6.5
pair_coeff 1 1 buck 3150.462646 0.35032282 626.7519553
pair_coeff 2 2 buck 659.595398 0.38609055 26.836679
pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
pair_coeff 1 3 lj/cut 0.09087 3.613
pair_coeff 1 4 lj/cut 0.0344258 3.238
pair_coeff 2 3 lj/cut 0.1419429 3.1
pair_coeff 2 4 lj/cut 0.035857762359063315 1.932779 # same as water dimer
pair_coeff 3 3 lj/cut 0.0 3.4
pair_coeff 4 4 lj/cut 0.0 2.65
pair_coeff * * coul/cut
bond_style harmonic
bond_coeff 1 29.40 1.09
angle_style harmonic
angle_coeff 1 0.172325 109.5
# remove bonds/angles in QM methane molecule
delete_bonds qm multi remove special
System init for delete_bonds ...
Generated 0 of 6 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 = 8.5
ghost atom cutoff = 8.5
binsize = 4.25, bins = 3 3 3
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair buck, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Deleting bonds ...
0 total bonds, 0 turned on, 0 turned off
0 total angles, 0 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
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.000 seconds
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
velocity all create 300.0 458732
# QMMM dynamics with small timestep
# dynamic or frozen zeolite
#fix 1 all nve
fix 1 qm nve
fix 2 qm mdi/qmmm potential elements Si O C H
fix_modify 2 energy yes
timestep 0.0001
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong f_2 pe etotal press
thermo 1
variable p equal extract_setting(world_size)
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" extra "template.methane.nw methane.nw log.zeolite.pwdft.qmmm.plugin.$p" command "run 2"
run 2
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.612 | 9.612 | 9.612 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press
0 0 300 2.9471313 -106.25003 -1065.0377 -1171.2878 0 0 -198.98094 -1370.2687 -1367.3216 -636.94701
1 10.663086 299.91218 2.9462686 -106.24961 -1065.1058 -1171.3554 0 0 -198.90989 -1370.2653 -1367.3191 -659.482
2 20.069001 299.81521 2.945316 -106.24919 -1065.1818 -1171.431 0 0 -198.83143 -1370.2624 -1367.3171 -684.54276
Loop time of 20.069 on 8 procs for 2 steps with 77 atoms
Performance: 0.001 ns/day, 27873.676 hours/ns, 0.100 timesteps/s, 7.674 atom-step/s
97.7% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.7853e-05 | 7.1816e-05 | 0.00015043 | 0.0 | 0.00
Bond | 2.509e-06 | 3.1355e-06 | 4.813e-06 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.6476e-05 | 0.00015375 | 0.00018447 | 0.0 | 0.00
Output | 8.3258e-05 | 8.9853e-05 | 0.00010303 | 0.0 | 0.00
Modify | 20.069 | 20.069 | 20.069 | 0.0 |100.00
Other | | 4.15e-05 | | | 0.00
Nlocal: 9.625 ave 20 max 3 min
Histogram: 1 2 1 0 1 2 0 0 0 1
Nghost: 426.375 ave 434 max 415 min
Histogram: 1 0 0 0 3 0 0 2 1 1
Neighs: 393.25 ave 941 max 132 min
Histogram: 2 2 0 1 2 0 0 0 0 1
Total # of neighbors = 3146
Ave neighs/atom = 40.857143
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:47

26
examples/QUANTUM/NWChem/nwchem_mdi.py
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@ -1,4 +1,4 @@
# MDI wrapper on NWChem PWDFT code
# MDI wrapper on NWChem PWDFT code
# NOTE: Qs or issues to still address
# test if works for both AIMD and QMMM
@ -11,7 +11,7 @@
# allow for box size changes, e.g. every step for NPT
# check NWC func call error returns ?
import sys,time
import sys,os,time
from ctypes import *
import numpy as np
@ -128,7 +128,7 @@ def options(other_options):
# --------------------------------------------
def mdi_engine(other_options):
global world,MPI_Comm,libpwdft
global world,me,nprocs,MPI_Comm,libpwdft
# get the MPI intra-communicator for this engine
@ -472,8 +472,12 @@ def evaluate():
error("QM atom properties not fully specified")
# setup new system within PWDFT
if new_system: pwdft_initialize()
# remove nwchemex.movecs file if it exists
if new_system:
if me == 0:
if os.path.exists("nwchemex.movecs"): os.remove("nwchemex.movecs")
pwdft_initialize()
# QMMM with QM and MM atoms
@ -483,7 +487,7 @@ def evaluate():
c_nw_outfile = nw_outfile.encode()
if mode == QMMM:
print("QMMM minimizer")
#print("QMMM minimizer")
time1 = time.time()
nwerr = libpwdft.\
c_lammps_pspw_qmmm_minimizer_filename(c_world,qm_coords,qm_potential,
@ -492,7 +496,7 @@ def evaluate():
# NOTE: check nwerr return?
qm_pe = c_qm_pe.value
time2 = time.time()
print("DONE QMMM minimizer",nwerr,time2-time1)
if me == 0: print("Time for PWDFT qmmm:",time2-time1)
#print("PE",qm_pe)
#print("FORCE",qm_forces)
#print("CHARGES",qm_charges)
@ -500,7 +504,7 @@ def evaluate():
# AIMD with only QM atoms
elif mode == AIMD:
print("AIMD minimizer")
#print("AIMD minimizer")
time1 = time.time()
nwerr = libpwdft.\
c_lammps_pspw_aimd_minimizer_filename(c_world,qm_coords,qm_forces,
@ -508,7 +512,7 @@ def evaluate():
# NOTE: check nwerr return?
qm_pe = c_qm_pe.value
time2 = time.time()
print("DONE AIMD minimizer",nwerr,time2-time1)
if me == 0: print("Time for PWDFT aimd:",time2-time1)
# clear flags for all MDI commands for next QM evaluation
@ -597,11 +601,11 @@ def pwdft_initialize():
infile = nw_infile.encode()
outfile = nw_outfile.encode()
print("INPUT filename")
#print("INPUT filename")
time1 = time.time()
nwerr = libpwdft.c_lammps_pspw_input_filename(c_world,infile,outfile)
time2 = time.time()
print("DONE INPUT filename",nwerr,time2-time1)
if me == 0: print("Time for PWDFT setup:",time2-time1)
# --------------------------------------------
# function called by MDI driver