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Fix sign of forces in AO mode, update h2o examples

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This commit is contained in:
jboschen
2020-01-31 00:42:00 -06:00
parent b9d68f93af
commit bc3807aa4b
18 changed files with 899 additions and 3988 deletions
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6
examples/COUPLE/lammps_nwchem/ao_basis/in.client.h2o
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@ -7,10 +7,6 @@ if "${mode} == file" then &
elif "${mode} == zmq" & elif "${mode} == zmq" &
"message client md zmq localhost:5555" & "message client md zmq localhost:5555" &
variable x index 1
variable y index 1
variable z index 1
units metal units metal
atom_style atomic atom_style atomic
atom_modify sort 0 0.0 map yes atom_modify sort 0 0.0 map yes
@ -18,8 +14,6 @@ atom_modify sort 0 0.0 map yes
boundary m m m boundary m m m
read_data data.h2o read_data data.h2o
replicate $x $y $z
velocity all create 300.0 87287 loop geom velocity all create 300.0 87287 loop geom
neighbor 0.3 bin neighbor 0.3 bin

9
examples/COUPLE/lammps_nwchem/lammps_nwchem/ao_basis/in.client.h2o → examples/COUPLE/lammps_nwchem/ao_basis/in.client.h2o.min
View File

@ -7,10 +7,6 @@ if "${mode} == file" then &
elif "${mode} == zmq" & elif "${mode} == zmq" &
"message client md zmq localhost:5555" & "message client md zmq localhost:5555" &
variable x index 1
variable y index 1
variable z index 1
units metal units metal
atom_style atomic atom_style atomic
atom_modify sort 0 0.0 map yes atom_modify sort 0 0.0 map yes
@ -18,7 +14,8 @@ atom_modify sort 0 0.0 map yes
boundary m m m boundary m m m
read_data data.h2o read_data data.h2o
replicate $x $y $z group one id 2
displace_atoms one move 0.1 0.2 0.3
velocity all create 300.0 87287 loop geom velocity all create 300.0 87287 loop geom
@ -30,4 +27,4 @@ fix 2 all client/md
fix_modify 2 energy yes fix_modify 2 energy yes
thermo 1 thermo 1
run 3 minimize 1.0e-6 1.0e-6 10 50

47
examples/COUPLE/lammps_nwchem/ao_basis/log.client.output
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@ -1,16 +1,12 @@
LAMMPS (18 Sep 2018) LAMMPS (19 Sep 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# H2O with NWChem # H2O with NWChem
variable mode index file variable mode index file
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
message client md zmq localhost:5555 message client md file tmp.couple
variable x index 1
variable y index 1
variable z index 1
units metal units metal
atom_style atomic atom_style atomic
atom_modify sort 0 0.0 map yes atom_modify sort 0 0.0 map yes
@ -21,15 +17,7 @@ read_data data.h2o
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
reading atoms ... reading atoms ...
3 atoms 3 atoms
read_data CPU = 0.000627125 secs
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
3 atoms
Time spent = 5.8016e-05 secs
velocity all create 300.0 87287 loop geom velocity all create 300.0 87287 loop geom
@ -42,26 +30,27 @@ fix_modify 2 energy yes
thermo 1 thermo 1
run 3 run 3
Per MPI rank memory allocation (min/avg/max) = 0.02705 | 0.02705 | 0.02705 Mbytes WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
Per MPI rank memory allocation (min/avg/max) = 0.0276 | 0.0276 | 0.0276 Mbytes
Step Temp E_pair E_mol TotEng Press Volume Step Temp E_pair E_mol TotEng Press Volume
0 300 0 0 -2068.2746 10.354878 8000 0 300 0 0 0.077556087 10.354878 8000
1 368.98118 0 0 -2068.2567 12.735851 8000 1 300 0 0 0.077556087 10.354878 8000
2 459.96278 0 0 -2068.2332 15.876195 8000 2 300 0 0 0.077556087 10.354878 8000
3 572.94479 0 0 -2068.204 19.775912 8000 3 300 0 0 0.077556087 10.354878 8000
Loop time of 0.0174769 on 1 procs for 3 steps with 3 atoms Loop time of 0.30198 on 1 procs for 3 steps with 3 atoms
Performance: 14.831 ns/day, 1.618 hours/ns, 171.655 timesteps/s Performance: 0.858 ns/day, 27.961 hours/ns, 9.934 timesteps/s
8.4% CPU use with 1 MPI tasks x 1 OpenMP threads 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.555e-06 | 2.555e-06 | 2.555e-06 | 0.0 | 0.01 Comm | 2.5979e-06 | 2.5979e-06 | 2.5979e-06 | 0.0 | 0.00
Output | 8.4169e-05 | 8.4169e-05 | 8.4169e-05 | 0.0 | 0.48 Output | 0.00012053 | 0.00012053 | 0.00012053 | 0.0 | 0.04
Modify | 0.017383 | 0.017383 | 0.017383 | 0.0 | 99.46 Modify | 0.30185 | 0.30185 | 0.30185 | 0.0 | 99.96
Other | | 7.694e-06 | | | 0.04 Other | | 8.211e-06 | | | 0.00
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -74,4 +63,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0 Ave neighs/atom = 0
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds not checked Dangerous builds not checked
Total wall time: 0:00:01 Total wall time: 0:00:07

45
examples/COUPLE/lammps_nwchem/lammps_nwchem/ao_basis/log.client.output → examples/COUPLE/lammps_nwchem/ao_basis/log.lammps.h2o.31Jan20
View File

@ -1,16 +1,12 @@
LAMMPS (18 Sep 2018) LAMMPS (19 Sep 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# H2O with NWChem # H2O with NWChem
variable mode index file variable mode index file
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
message client md zmq localhost:5555 message client md file tmp.couple
variable x index 1
variable y index 1
variable z index 1
units metal units metal
atom_style atomic atom_style atomic
atom_modify sort 0 0.0 map yes atom_modify sort 0 0.0 map yes
@ -21,15 +17,7 @@ read_data data.h2o
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
reading atoms ... reading atoms ...
3 atoms 3 atoms
read_data CPU = 0.000608759 secs
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
3 atoms
Time spent = 5.8016e-05 secs
velocity all create 300.0 87287 loop geom velocity all create 300.0 87287 loop geom
@ -42,26 +30,27 @@ fix_modify 2 energy yes
thermo 1 thermo 1
run 3 run 3
Per MPI rank memory allocation (min/avg/max) = 0.02705 | 0.02705 | 0.02705 Mbytes WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
Per MPI rank memory allocation (min/avg/max) = 0.0276 | 0.0276 | 0.0276 Mbytes
Step Temp E_pair E_mol TotEng Press Volume Step Temp E_pair E_mol TotEng Press Volume
0 300 0 0 -2068.2746 10.354878 8000 0 300 0 0 -2068.2746 10.354878 8000
1 368.98118 0 0 -2068.2567 12.735851 8000 1 200.33191 0 0 -2068.2704 6.9147085 8000
2 459.96278 0 0 -2068.2332 15.876195 8000 2 152.36218 0 0 -2068.269 5.2589726 8000
3 572.94479 0 0 -2068.204 19.775912 8000 3 227.40679 0 0 -2068.2722 7.8492321 8000
Loop time of 0.0174769 on 1 procs for 3 steps with 3 atoms Loop time of 1.90319 on 1 procs for 3 steps with 3 atoms
Performance: 14.831 ns/day, 1.618 hours/ns, 171.655 timesteps/s Performance: 0.136 ns/day, 176.221 hours/ns, 1.576 timesteps/s
8.4% CPU use with 1 MPI tasks x 1 OpenMP threads 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.555e-06 | 2.555e-06 | 2.555e-06 | 0.0 | 0.01 Comm | 3.9274e-06 | 3.9274e-06 | 3.9274e-06 | 0.0 | 0.00
Output | 8.4169e-05 | 8.4169e-05 | 8.4169e-05 | 0.0 | 0.48 Output | 0.00011798 | 0.00011798 | 0.00011798 | 0.0 | 0.01
Modify | 0.017383 | 0.017383 | 0.017383 | 0.0 | 99.46 Modify | 1.9031 | 1.9031 | 1.9031 | 0.0 | 99.99
Other | | 7.694e-06 | | | 0.04 Other | | 1.054e-05 | | | 0.00
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -74,4 +63,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0 Ave neighs/atom = 0
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds not checked Dangerous builds not checked
Total wall time: 0:00:01 Total wall time: 0:00:07

82
examples/COUPLE/lammps_nwchem/ao_basis/log.lammps.h2o.min.31Jan20 Normal file
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@ -0,0 +1,82 @@
LAMMPS (19 Sep 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
using 1 OpenMP thread(s) per MPI task
# H2O with NWChem
variable mode index file
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
message client md file tmp.couple
units metal
atom_style atomic
atom_modify sort 0 0.0 map yes
boundary m m m
read_data data.h2o
orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
3 atoms
read_data CPU = 0.000615383 secs
group one id 2
1 atoms in group one
displace_atoms one move 0.1 0.2 0.3
velocity all create 300.0 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 10 check no
fix 1 all nve
fix 2 all client/md
fix_modify 2 energy yes
thermo 1
minimize 1.0e-6 1.0e-6 10 50
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:174)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
Per MPI rank memory allocation (min/avg/max) = 0.0279 | 0.0279 | 0.0279 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 0 0 -2067.8909 10.354878 8000
1 300 0 0 -2068.0707 10.354878 8000
2 300 0 0 -2068.252 10.354878 8000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
3 300 0 0 -2068.2797 10.354878 8000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
4 300 0 0 -2068.2799 10.354878 8000
Loop time of 5.71024 on 1 procs for 4 steps with 3 atoms
0.1% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2067.96847053 -2068.35730416 -2068.35745184
Force two-norm initial, final = 4.54685 0.124714
Force max component initial, final = 3.48924 0.0859263
Final line search alpha, max atom move = 1 0.0859263
Iterations, force evaluations = 4 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 6.2305e-07 | 6.2305e-07 | 6.2305e-07 | 0.0 | 0.00
Comm | 1.1522e-05 | 1.1522e-05 | 1.1522e-05 | 0.0 | 0.00
Output | 8.4217e-05 | 8.4217e-05 | 8.4217e-05 | 0.0 | 0.00
Modify | 5.7099 | 5.7099 | 5.7099 | 0.0 | 99.99
Other | | 0.0002355 | | | 0.00
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 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 = 2
Dangerous builds not checked
Total wall time: 0:00:10

622
examples/COUPLE/lammps_nwchem/ao_basis/nwchem_lammps.out
View File

@ -1,622 +0,0 @@
argument 1 = nwchem_lammps.nw
============================== echo of input deck ==============================
echo
memory global 40 mb stack 23 mb heap 5 mb
geometry units angstrom noautosym
O 0 0 0
H 0 0.756723 -0.585799
H 0 -0.756723 -0.585799
end
scf
vectors input nwchem_lammps.movecs
end
dft
vectors input nwchem_lammps.movecs
end
basis
O library 6-31g*
H library 6-31g*
end
scf
maxiter 100
end
task scf gradient
================================================================================
Northwest Computational Chemistry Package (NWChem) 6.8
------------------------------------------------------
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352
Copyright (c) 1994-2017
Pacific Northwest National Laboratory
Battelle Memorial Institute
NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file
ACKNOWLEDGMENT
--------------
This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.
Job information
---------------
hostname = mcq
program = /usr/bin/nwchem
date = Mon Sep 23 16:28:27 2019
compiled = Wed_Aug_15_19:14:19_2018
source = /home/edo/debichem-team/nwchem/nwchem-6.8.1
nwchem branch = 6.8.1
nwchem revision = v6.8-133-ge032219
ga revision = 5.6.5
use scalapack = T
input = nwchem_lammps.nw
prefix = nwchem_lammps.
data base = ./nwchem_lammps.db
status = restart
nproc = 1
time left = -1s
Memory information
------------------
heap = 655358 doubles = 5.0 Mbytes
stack = 3014651 doubles = 23.0 Mbytes
global = 5242880 doubles = 40.0 Mbytes (distinct from heap & stack)
total = 8912889 doubles = 68.0 Mbytes
verify = yes
hardfail = no
Directory information
---------------------
0 permanent = .
0 scratch = .
Previous task information
-------------------------
Theory = scf
Operation = gradient
Status = ok
Qmmm = F
Ignore = F
Geometries in the database
--------------------------
Name Natoms Last Modified
-------------------------------- ------ ------------------------
1 geometry 3 Mon Sep 23 16:26:29 2019
The geometry named "geometry" is the default for restart
Basis sets in the database
--------------------------
Name Natoms Last Modified
-------------------------------- ------ ------------------------
1 ao basis 2 Mon Sep 23 16:26:29 2019
The basis set named "ao basis" is the default AO basis for restart
NWChem Input Module
-------------------
Scaling coordinates for geometry "geometry" by 1.889725989
(inverse scale = 0.529177249)
------
auto-z
------
Geometry "geometry" -> ""
-------------------------
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 O 8.0000 0.00000000 0.00000000 0.11715980
2 H 1.0000 0.00000000 0.75672300 -0.46863920
3 H 1.0000 0.00000000 -0.75672300 -0.46863920
Atomic Mass
-----------
O 15.994910
H 1.007825
Effective nuclear repulsion energy (a.u.) 9.1972032776
Nuclear Dipole moment (a.u.)
----------------------------
X Y Z
---------------- ---------------- ----------------
0.0000000000 0.0000000000 0.0000000000
Z-matrix (autoz)
--------
Units are Angstrom for bonds and degrees for angles
Type Name I J K L M Value
----------- -------- ----- ----- ----- ----- ----- ----------
1 Stretch 1 2 0.95697
2 Stretch 1 3 0.95697
3 Bend 2 1 3 104.51122
XYZ format geometry
-------------------
3
geometry
O 0.00000000 0.00000000 0.11715980
H 0.00000000 0.75672300 -0.46863920
H 0.00000000 -0.75672300 -0.46863920
==============================================================================
internuclear distances
------------------------------------------------------------------------------
center one | center two | atomic units | angstroms
------------------------------------------------------------------------------
2 H | 1 O | 1.80841 | 0.95697
3 H | 1 O | 1.80841 | 0.95697
------------------------------------------------------------------------------
number of included internuclear distances: 2
==============================================================================
==============================================================================
internuclear angles
------------------------------------------------------------------------------
center 1 | center 2 | center 3 | degrees
------------------------------------------------------------------------------
2 H | 1 O | 3 H | 104.51
------------------------------------------------------------------------------
number of included internuclear angles: 1
==============================================================================
Basis "ao basis" -> "" (cartesian)
-----
O (Oxygen)
----------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 5.48467170E+03 0.001831
1 S 8.25234950E+02 0.013950
1 S 1.88046960E+02 0.068445
1 S 5.29645000E+01 0.232714
1 S 1.68975700E+01 0.470193
1 S 5.79963530E+00 0.358521
2 S 1.55396160E+01 -0.110778
2 S 3.59993360E+00 -0.148026
2 S 1.01376180E+00 1.130767
3 P 1.55396160E+01 0.070874
3 P 3.59993360E+00 0.339753
3 P 1.01376180E+00 0.727159
4 S 2.70005800E-01 1.000000
5 P 2.70005800E-01 1.000000
6 D 8.00000000E-01 1.000000
H (Hydrogen)
------------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 1.87311370E+01 0.033495
1 S 2.82539370E+00 0.234727
1 S 6.40121700E-01 0.813757
2 S 1.61277800E-01 1.000000
Summary of "ao basis" -> "" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
O 6-31g* 6 15 3s2p1d
H 6-31g* 2 2 2s
NWChem SCF Module
-----------------
ao basis = "ao basis"
functions = 19
atoms = 3
closed shells = 5
open shells = 0
charge = 0.00
wavefunction = RHF
input vectors = ./nwchem_lammps.movecs
output vectors = ./nwchem_lammps.movecs
use symmetry = F
symmetry adapt = F
Summary of "ao basis" -> "ao basis" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
O 6-31g* 6 15 3s2p1d
H 6-31g* 2 2 2s
Forming initial guess at 0.0s
Loading old vectors from job with title :
Starting SCF solution at 0.0s
----------------------------------------------
Quadratically convergent ROHF
Convergence threshold : 1.000E-04
Maximum no. of iterations : 100
Final Fock-matrix accuracy: 1.000E-07
----------------------------------------------
#quartets = 1.540D+03 #integrals = 8.874D+03 #direct = 0.0% #cached =100.0%
Integral file = ./nwchem_lammps.aoints.0
Record size in doubles = 65536 No. of integs per rec = 43688
Max. records in memory = 2 Max. records in file = 326674
No. of bits per label = 8 No. of bits per value = 64
iter energy gnorm gmax time
----- ------------------- --------- --------- --------
1 -75.9732571733 7.14D-01 3.37D-01 0.3
2 -76.0055117003 3.10D-01 1.79D-01 0.3
3 -76.0098071888 1.15D-01 5.21D-02 0.3
4 -76.0105377099 2.55D-03 9.57D-04 0.3
5 -76.0105386346 9.48D-06 3.52D-06 0.3
Final RHF results
------------------
Total SCF energy = -76.010538634624
One-electron energy = -123.058850386783
Two-electron energy = 37.851108474513
Nuclear repulsion energy = 9.197203277646
Time for solution = 0.1s
Final eigenvalues
-----------------
1
1 -20.5603
2 -1.3419
3 -0.7071
4 -0.5711
5 -0.4979
6 0.2108
7 0.3042
8 1.0227
9 1.1318
10 1.1678
11 1.1719
12 1.3809
13 1.4341
14 2.0201
15 2.0337
ROHF Final Molecular Orbital Analysis
-------------------------------------
Vector 2 Occ=2.000000D+00 E=-1.341930D+00
MO Center= -7.7D-08, 1.6D-07, -5.6D-02, r^2= 5.0D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
2 0.475861 1 O s 6 0.439201 1 O s
1 -0.209676 1 O s
Vector 3 Occ=2.000000D+00 E=-7.070591D-01
MO Center= 5.8D-08, -1.2D-07, -1.0D-01, r^2= 7.7D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
4 0.507651 1 O py 8 0.306488 1 O py
16 0.230979 2 H s 18 -0.230979 3 H s
Vector 4 Occ=2.000000D+00 E=-5.710712D-01
MO Center= 6.9D-07, -2.0D-07, 1.7D-01, r^2= 6.9D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
5 0.555446 1 O pz 9 0.403175 1 O pz
6 0.325535 1 O s 2 0.164591 1 O s
Vector 5 Occ=2.000000D+00 E=-4.979251D-01
MO Center= -9.5D-08, -7.1D-08, 9.7D-02, r^2= 6.0D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
3 0.639615 1 O px 7 0.511470 1 O px
Vector 6 Occ=0.000000D+00 E= 2.108019D-01
MO Center= -5.7D-07, 1.0D-06, -6.5D-01, r^2= 2.6D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
6 1.415545 1 O s 17 -1.041449 2 H s
19 -1.041447 3 H s 9 -0.508218 1 O pz
5 -0.217054 1 O pz
Vector 7 Occ=0.000000D+00 E= 3.042327D-01
MO Center= -1.9D-09, -9.8D-07, -6.2D-01, r^2= 2.7D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
17 1.395012 2 H s 19 -1.395014 3 H s
8 -0.833805 1 O py 4 -0.329272 1 O py
Vector 8 Occ=0.000000D+00 E= 1.022735D+00
MO Center= -1.1D-10, 6.2D-07, -4.7D-02, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
16 0.838912 2 H s 18 -0.838911 3 H s
8 -0.662620 1 O py 17 -0.459236 2 H s
19 0.459235 3 H s 14 -0.343167 1 O dyz
Vector 9 Occ=0.000000D+00 E= 1.131842D+00
MO Center= 2.2D-07, 3.1D-07, 2.0D-01, r^2= 1.6D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
6 1.636696 1 O s 2 -0.921950 1 O s
9 0.708679 1 O pz 16 0.548799 2 H s
18 0.548800 3 H s 17 -0.474050 2 H s
19 -0.474049 3 H s 5 -0.419243 1 O pz
10 -0.387486 1 O dxx 15 -0.318053 1 O dzz
Vector 10 Occ=0.000000D+00 E= 1.167786D+00
MO Center= 2.2D-05, 5.1D-09, 1.1D-01, r^2= 1.1D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
7 -1.036049 1 O px 3 0.962745 1 O px
Vector 11 Occ=0.000000D+00 E= 1.171944D+00
MO Center= -2.2D-05, -4.7D-07, -3.9D-02, r^2= 1.1D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
5 0.761007 1 O pz 16 0.661205 2 H s
18 0.661206 3 H s 6 -0.462694 1 O s
9 -0.370404 1 O pz 17 -0.357353 2 H s
19 -0.357353 3 H s 13 0.249348 1 O dyy
Vector 12 Occ=0.000000D+00 E= 1.380937D+00
MO Center= -2.5D-09, 2.4D-07, 5.7D-02, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
8 1.537091 1 O py 4 -1.037376 1 O py
17 -0.915091 2 H s 19 0.915090 3 H s
Vector 13 Occ=0.000000D+00 E= 1.434077D+00
MO Center= 5.4D-08, -5.6D-07, -3.9D-01, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
6 3.574401 1 O s 2 -1.418426 1 O s
9 -1.174649 1 O pz 17 -0.784923 2 H s
19 -0.784925 3 H s 13 -0.644454 1 O dyy
5 0.506381 1 O pz 15 -0.402328 1 O dzz
16 -0.323132 2 H s 18 -0.323132 3 H s
Vector 14 Occ=0.000000D+00 E= 2.020054D+00
MO Center= -2.1D-08, 1.2D-08, 1.6D-01, r^2= 6.2D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
15 1.008815 1 O dzz 13 -0.580616 1 O dyy
10 -0.366779 1 O dxx 6 -0.227333 1 O s
Vector 15 Occ=0.000000D+00 E= 2.033720D+00
MO Center= -5.0D-08, 6.6D-08, 1.2D-01, r^2= 6.1D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
11 1.732051 1 O dxy
center of mass
--------------
x = 0.00000000 y = 0.00000000 z = 0.09751017
moments of inertia (a.u.)
------------------
6.315433940446 0.000000000000 0.000000000000
0.000000000000 2.193636332720 0.000000000000
0.000000000000 0.000000000000 4.121797607726
Mulliken analysis of the total density
--------------------------------------
Atom Charge Shell Charges
----------- ------ -------------------------------------------------------
1 O 8 8.87 2.00 0.90 2.90 0.92 2.07 0.08
2 H 1 0.57 0.46 0.10
3 H 1 0.57 0.46 0.10
Multipole analysis of the density wrt the origin
------------------------------------------------
L x y z total open nuclear
- - - - ----- ---- -------
0 0 0 0 0.000000 0.000000 10.000000
1 1 0 0 -0.000002 0.000000 0.000000
1 0 1 0 0.000001 0.000000 0.000000
1 0 0 1 -0.875296 0.000000 0.000000
2 2 0 0 -5.372336 0.000000 0.000000
2 1 1 0 -0.000002 0.000000 0.000000
2 1 0 1 0.000001 0.000000 0.000000
2 0 2 0 -3.071804 0.000000 4.089795
2 0 1 1 0.000000 0.000000 0.000000
2 0 0 2 -4.444596 0.000000 1.960717
Parallel integral file used 1 records with 0 large values
NWChem Gradients Module
-----------------------
wavefunction = RHF
RHF ENERGY GRADIENTS
atom coordinates gradient
x y z x y z
1 O 0.000000 0.000000 0.221400 0.000001 0.000000 0.014490
2 H 0.000000 1.429999 -0.885600 -0.000001 0.007296 -0.007245
3 H 0.000000 -1.429999 -0.885600 -0.000000 -0.007296 -0.007245
----------------------------------------
| Time | 1-e(secs) | 2-e(secs) |
----------------------------------------
| CPU | 0.00 | 0.07 |
----------------------------------------
| WALL | 0.00 | 0.03 |
----------------------------------------
Task times cpu: 0.2s wall: 0.1s
NWChem Input Module
-------------------
Summary of allocated global arrays
-----------------------------------
No active global arrays
GA Statistics for process 0
------------------------------
create destroy get put acc scatter gather read&inc
calls: 225 225 3182 894 878 0 0 68
number of processes/call 1.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00
bytes total: 8.62e+05 5.44e+05 1.23e+05 0.00e+00 0.00e+00 5.44e+02
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
Max memory consumed for GA by this process: 39432 bytes
MA_summarize_allocated_blocks: starting scan ...
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
MA usage statistics:
allocation statistics:
heap stack
---- -----
current number of blocks 0 0
maximum number of blocks 18 28
current total bytes 0 0
maximum total bytes 1060104 16000888
maximum total K-bytes 1061 16001
maximum total M-bytes 2 17
CITATION
--------
Please cite the following reference when publishing
results obtained with NWChem:
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
E. Apra, T.L. Windus, W.A. de Jong
"NWChem: a comprehensive and scalable open-source
solution for large scale molecular simulations"
Comput. Phys. Commun. 181, 1477 (2010)
doi:10.1016/j.cpc.2010.04.018
AUTHORS
-------
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
Total times cpu: 0.2s wall: 0.1s

298
examples/COUPLE/lammps_nwchem/lammps_nwchem/ao_basis/nwchem_lammps.out → examples/COUPLE/lammps_nwchem/ao_basis/nwchem_lammps.out.h2o.31Jan20
View File

@ -7,10 +7,10 @@ echo
memory global 40 mb stack 23 mb heap 5 mb memory global 40 mb stack 23 mb heap 5 mb
geometry units angstrom noautosym geometry units angstrom noautosym nocenter
O 0 0 0 O 0.00197082 0.0012463 -0.00298048
H 0 0.756723 -0.585799 H -0.0432066 0.769363 -0.596119
H 0 -0.756723 -0.585799 H 0.0119282 -0.789143 -0.528177
end end
scf scf
@ -30,8 +30,12 @@ scf
maxiter 100 maxiter 100
end end
task scf gradient #dft
# xc b3lyp
#end
task scf gradient
#task dft gradient
================================================================================ ================================================================================
@ -47,7 +51,7 @@ task scf gradient
Pacific Northwest National Laboratory Pacific Northwest National Laboratory
Richland, WA 99352 Richland, WA 99352
Copyright (c) 1994-2017 Copyright (c) 1994-2018
Pacific Northwest National Laboratory Pacific Northwest National Laboratory
Battelle Memorial Institute Battelle Memorial Institute
@ -72,16 +76,16 @@ task scf gradient
Job information Job information
--------------- ---------------
hostname = mcq hostname = almondjoy
program = /usr/bin/nwchem program = /home/jboschen/nwchem-6.8.1-release/bin/LINUX64/nwchem
date = Mon Sep 23 16:28:27 2019 date = Fri Jan 31 00:31:00 2020
compiled = Wed_Aug_15_19:14:19_2018 compiled = Tue_Oct_01_13:20:43_2019
source = /home/edo/debichem-team/nwchem/nwchem-6.8.1 source = /home/jboschen/nwchem-6.8.1-release
nwchem branch = 6.8.1 nwchem branch = Development
nwchem revision = v6.8-133-ge032219 nwchem revision = N/A
ga revision = 5.6.5 ga revision = 5.6.5
use scalapack = T use scalapack = F
input = nwchem_lammps.nw input = nwchem_lammps.nw
prefix = nwchem_lammps. prefix = nwchem_lammps.
data base = ./nwchem_lammps.db data base = ./nwchem_lammps.db
@ -124,7 +128,7 @@ task scf gradient
Name Natoms Last Modified Name Natoms Last Modified
-------------------------------- ------ ------------------------ -------------------------------- ------ ------------------------
1 geometry 3 Mon Sep 23 16:26:29 2019 1 geometry 3 Fri Jan 31 00:30:59 2020
The geometry named "geometry" is the default for restart The geometry named "geometry" is the default for restart
@ -135,7 +139,7 @@ task scf gradient
Name Natoms Last Modified Name Natoms Last Modified
-------------------------------- ------ ------------------------ -------------------------------- ------ ------------------------
1 ao basis 2 Mon Sep 23 16:26:29 2019 1 ao basis 2 Fri Jan 31 00:30:59 2020
The basis set named "ao basis" is the default AO basis for restart The basis set named "ao basis" is the default AO basis for restart
@ -154,6 +158,8 @@ task scf gradient
------ ------
auto-z auto-z
------ ------
no constraints, skipping 0.0000000000000000
no constraints, skipping 0.0000000000000000
Geometry "geometry" -> "" Geometry "geometry" -> ""
@ -163,9 +169,9 @@ task scf gradient
No. Tag Charge X Y Z No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- -------------- ---- ---------------- ---------- -------------- -------------- --------------
1 O 8.0000 0.00000000 0.00000000 0.11715980 1 O 8.0000 0.00197082 0.00124630 -0.00298048
2 H 1.0000 0.00000000 0.75672300 -0.46863920 2 H 1.0000 -0.04320660 0.76936300 -0.59611900
3 H 1.0000 0.00000000 -0.75672300 -0.46863920 3 H 1.0000 0.01192820 -0.78914300 -0.52817700
Atomic Mass Atomic Mass
----------- -----------
@ -174,13 +180,13 @@ task scf gradient
H 1.007825 H 1.007825
Effective nuclear repulsion energy (a.u.) 9.1972032776 Effective nuclear repulsion energy (a.u.) 9.1573270473
Nuclear Dipole moment (a.u.) Nuclear Dipole moment (a.u.)
---------------------------- ----------------------------
X Y Z X Y Z
---------------- ---------------- ---------------- ---------------- ---------------- ----------------
0.0000000000 0.0000000000 0.0000000000 -0.0293131272 -0.0185374561 -2.1696696942
@ -191,26 +197,26 @@ task scf gradient
Type Name I J K L M Value Type Name I J K L M Value
----------- -------- ----- ----- ----- ----- ----- ---------- ----------- -------- ----- ----- ----- ----- ----- ----------
1 Stretch 1 2 0.95697 1 Stretch 1 2 0.97152
2 Stretch 1 3 0.95697 2 Stretch 1 3 0.94902
3 Bend 2 1 3 104.51122 3 Bend 2 1 3 108.72901
XYZ format geometry XYZ format geometry
------------------- -------------------
3 3
geometry geometry
O 0.00000000 0.00000000 0.11715980 O 0.00197082 0.00124630 -0.00298048
H 0.00000000 0.75672300 -0.46863920 H -0.04320660 0.76936300 -0.59611900
H 0.00000000 -0.75672300 -0.46863920 H 0.01192820 -0.78914300 -0.52817700
============================================================================== ==============================================================================
internuclear distances internuclear distances
------------------------------------------------------------------------------ ------------------------------------------------------------------------------
center one | center two | atomic units | angstroms center one | center two | atomic units | angstroms
------------------------------------------------------------------------------ ------------------------------------------------------------------------------
2 H | 1 O | 1.80841 | 0.95697 2 H | 1 O | 1.83591 | 0.97152
3 H | 1 O | 1.80841 | 0.95697 3 H | 1 O | 1.79339 | 0.94902
------------------------------------------------------------------------------ ------------------------------------------------------------------------------
number of included internuclear distances: 2 number of included internuclear distances: 2
============================================================================== ==============================================================================
@ -222,7 +228,7 @@ task scf gradient
------------------------------------------------------------------------------ ------------------------------------------------------------------------------
center 1 | center 2 | center 3 | degrees center 1 | center 2 | center 3 | degrees
------------------------------------------------------------------------------ ------------------------------------------------------------------------------
2 H | 1 O | 3 H | 104.51 2 H | 1 O | 3 H | 108.73
------------------------------------------------------------------------------ ------------------------------------------------------------------------------
number of included internuclear angles: 1 number of included internuclear angles: 1
============================================================================== ==============================================================================
@ -324,200 +330,198 @@ task scf gradient
---------------------------------------------- ----------------------------------------------
#quartets = 1.540D+03 #integrals = 8.874D+03 #direct = 0.0% #cached =100.0% #quartets = 1.540D+03 #integrals = 1.424D+04 #direct = 0.0% #cached =100.0%
Integral file = ./nwchem_lammps.aoints.0 Integral file = ./nwchem_lammps.aoints.0
Record size in doubles = 65536 No. of integs per rec = 43688 Record size in doubles = 65536 No. of integs per rec = 43688
Max. records in memory = 2 Max. records in file = 326674 Max. records in memory = 2 Max. records in file = 1392051
No. of bits per label = 8 No. of bits per value = 64 No. of bits per label = 8 No. of bits per value = 64
iter energy gnorm gmax time iter energy gnorm gmax time
----- ------------------- --------- --------- -------- ----- ------------------- --------- --------- --------
1 -75.9732571733 7.14D-01 3.37D-01 0.3 1 -76.0095751323 4.63D-02 1.64D-02 0.1
2 -76.0055117003 3.10D-01 1.79D-01 0.3 2 -76.0097628164 8.13D-04 2.83D-04 0.1
3 -76.0098071888 1.15D-01 5.21D-02 0.3 3 -76.0097629130 3.92D-06 1.55D-06 0.1
4 -76.0105377099 2.55D-03 9.57D-04 0.3
5 -76.0105386346 9.48D-06 3.52D-06 0.3
Final RHF results Final RHF results
------------------ ------------------
Total SCF energy = -76.010538634624 Total SCF energy = -76.009762913030
One-electron energy = -123.058850386783 One-electron energy = -123.002897732381
Two-electron energy = 37.851108474513 Two-electron energy = 37.835807772101
Nuclear repulsion energy = 9.197203277646 Nuclear repulsion energy = 9.157327047250
Time for solution = 0.1s Time for solution = 0.0s
Final eigenvalues Final eigenvalues
----------------- -----------------
1 1
1 -20.5603 1 -20.5584
2 -1.3419 2 -1.3367
3 -0.7071 3 -0.7128
4 -0.5711 4 -0.5617
5 -0.4979 5 -0.4959
6 0.2108 6 0.2104
7 0.3042 7 0.3038
8 1.0227 8 1.0409
9 1.1318 9 1.1202
10 1.1678 10 1.1606
11 1.1719 11 1.1691
12 1.3809 12 1.3840
13 1.4341 13 1.4192
14 2.0201 14 2.0312
15 2.0337 15 2.0334
ROHF Final Molecular Orbital Analysis ROHF Final Molecular Orbital Analysis
------------------------------------- -------------------------------------
Vector 2 Occ=2.000000D+00 E=-1.341930D+00 Vector 2 Occ=2.000000D+00 E=-1.336749D+00
MO Center= -7.7D-08, 1.6D-07, -5.6D-02, r^2= 5.0D-01 MO Center= -2.8D-03, -1.3D-02, -1.7D-01, r^2= 5.1D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
2 0.475861 1 O s 6 0.439201 1 O s 2 0.476636 1 O s 6 0.442369 1 O s
1 -0.209676 1 O s 1 -0.210214 1 O s
Vector 3 Occ=2.000000D+00 E=-7.070591D-01 Vector 3 Occ=2.000000D+00 E=-7.127948D-01
MO Center= 5.8D-08, -1.2D-07, -1.0D-01, r^2= 7.7D-01 MO Center= -4.9D-03, 3.9D-03, -2.1D-01, r^2= 7.8D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
4 0.507651 1 O py 8 0.306488 1 O py 4 0.504894 1 O py 8 0.303932 1 O py
16 0.230979 2 H s 18 -0.230979 3 H s 18 -0.234724 3 H s 16 0.229765 2 H s
Vector 4 Occ=2.000000D+00 E=-5.710712D-01 Vector 4 Occ=2.000000D+00 E=-5.617306D-01
MO Center= 6.9D-07, -2.0D-07, 1.7D-01, r^2= 6.9D-01 MO Center= 3.6D-03, 9.0D-03, 5.6D-02, r^2= 6.9D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
5 0.555446 1 O pz 9 0.403175 1 O pz 5 0.559565 1 O pz 9 0.410981 1 O pz
6 0.325535 1 O s 2 0.164591 1 O s 6 0.315892 1 O s 2 0.157960 1 O s
Vector 5 Occ=2.000000D+00 E=-4.979251D-01 Vector 5 Occ=2.000000D+00 E=-4.959173D-01
MO Center= -9.5D-08, -7.1D-08, 9.7D-02, r^2= 6.0D-01 MO Center= 1.4D-03, 6.9D-05, -2.2D-02, r^2= 6.0D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
3 0.639615 1 O px 7 0.511470 1 O px 3 0.638390 1 O px 7 0.511530 1 O px
Vector 6 Occ=0.000000D+00 E= 2.108019D-01 Vector 6 Occ=0.000000D+00 E= 2.103822D-01
MO Center= -5.7D-07, 1.0D-06, -6.5D-01, r^2= 2.6D+00 MO Center= -2.3D-02, 3.5D-02, -7.3D-01, r^2= 2.6D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
6 1.415545 1 O s 17 -1.041449 2 H s 6 1.416869 1 O s 17 -1.068330 2 H s
19 -1.041447 3 H s 9 -0.508218 1 O pz 19 -1.014775 3 H s 9 -0.490951 1 O pz
5 -0.217054 1 O pz 5 -0.212990 1 O pz
Vector 7 Occ=0.000000D+00 E= 3.042327D-01 Vector 7 Occ=0.000000D+00 E= 3.037943D-01
MO Center= -1.9D-09, -9.8D-07, -6.2D-01, r^2= 2.7D+00 MO Center= -1.8D-02, -8.9D-02, -7.1D-01, r^2= 2.8D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
17 1.395012 2 H s 19 -1.395014 3 H s 19 -1.426837 3 H s 17 1.332767 2 H s
8 -0.833805 1 O py 4 -0.329272 1 O py 8 -0.842141 1 O py 4 -0.327553 1 O py
Vector 8 Occ=0.000000D+00 E= 1.022735D+00 Vector 8 Occ=0.000000D+00 E= 1.040852D+00
MO Center= -1.1D-10, 6.2D-07, -4.7D-02, r^2= 1.4D+00 MO Center= -7.4D-03, 1.3D-01, -1.6D-01, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
16 0.838912 2 H s 18 -0.838911 3 H s 16 0.931594 2 H s 18 -0.747590 3 H s
8 -0.662620 1 O py 17 -0.459236 2 H s 8 -0.655817 1 O py 17 -0.523035 2 H s
19 0.459235 3 H s 14 -0.343167 1 O dyz 19 0.366407 3 H s 14 -0.357109 1 O dyz
Vector 9 Occ=0.000000D+00 E= 1.131842D+00 Vector 9 Occ=0.000000D+00 E= 1.120172D+00
MO Center= 2.2D-07, 3.1D-07, 2.0D-01, r^2= 1.6D+00 MO Center= -6.8D-03, -2.9D-02, -3.1D-01, r^2= 1.5D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
6 1.636696 1 O s 2 -0.921950 1 O s 6 1.145090 1 O s 18 0.841596 3 H s
9 0.708679 1 O pz 16 0.548799 2 H s 2 -0.727471 1 O s 16 0.684927 2 H s
18 0.548800 3 H s 17 -0.474050 2 H s 9 0.559191 1 O pz 19 -0.546678 3 H s
19 -0.474049 3 H s 5 -0.419243 1 O pz 17 -0.538778 2 H s 10 -0.344609 1 O dxx
10 -0.387486 1 O dxx 15 -0.318053 1 O dzz 15 -0.250035 1 O dzz
Vector 10 Occ=0.000000D+00 E= 1.167786D+00 Vector 10 Occ=0.000000D+00 E= 1.160603D+00
MO Center= 2.2D-05, 5.1D-09, 1.1D-01, r^2= 1.1D+00 MO Center= 1.2D-02, -4.3D-02, 2.5D-01, r^2= 1.0D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
7 -1.036049 1 O px 3 0.962745 1 O px 6 1.137949 1 O s 5 -0.844233 1 O pz
9 0.595088 1 O pz 2 -0.475986 1 O s
18 -0.455932 3 H s 16 -0.357325 2 H s
13 -0.317117 1 O dyy 15 -0.196968 1 O dzz
Vector 11 Occ=0.000000D+00 E= 1.171944D+00 Vector 11 Occ=0.000000D+00 E= 1.169054D+00
MO Center= -2.2D-05, -4.7D-07, -3.9D-02, r^2= 1.1D+00 MO Center= 1.9D-03, 1.2D-03, -6.4D-03, r^2= 1.1D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
5 0.761007 1 O pz 16 0.661205 2 H s 7 -1.034653 1 O px 3 0.962043 1 O px
18 0.661206 3 H s 6 -0.462694 1 O s
9 -0.370404 1 O pz 17 -0.357353 2 H s
19 -0.357353 3 H s 13 0.249348 1 O dyy
Vector 12 Occ=0.000000D+00 E= 1.380937D+00 Vector 12 Occ=0.000000D+00 E= 1.384034D+00
MO Center= -2.5D-09, 2.4D-07, 5.7D-02, r^2= 1.4D+00 MO Center= 6.0D-04, -2.6D-03, -5.0D-02, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
8 1.537091 1 O py 4 -1.037376 1 O py 8 1.557767 1 O py 4 -1.035829 1 O py
17 -0.915091 2 H s 19 0.915090 3 H s 17 -0.900920 2 H s 19 0.901756 3 H s
Vector 13 Occ=0.000000D+00 E= 1.434077D+00 Vector 13 Occ=0.000000D+00 E= 1.419205D+00
MO Center= 5.4D-08, -5.6D-07, -3.9D-01, r^2= 1.4D+00 MO Center= -1.3D-02, -4.9D-02, -5.2D-01, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
6 3.574401 1 O s 2 -1.418426 1 O s 6 3.605136 1 O s 2 -1.454853 1 O s
9 -1.174649 1 O pz 17 -0.784923 2 H s 9 -1.107532 1 O pz 19 -0.874208 3 H s
19 -0.784925 3 H s 13 -0.644454 1 O dyy 17 -0.757016 2 H s 13 -0.634436 1 O dyy
5 0.506381 1 O pz 15 -0.402328 1 O dzz 5 0.516593 1 O pz 15 -0.401100 1 O dzz
16 -0.323132 2 H s 18 -0.323132 3 H s 10 -0.319873 1 O dxx 16 -0.260650 2 H s
Vector 14 Occ=0.000000D+00 E= 2.020054D+00 Vector 14 Occ=0.000000D+00 E= 2.031234D+00
MO Center= -2.1D-08, 1.2D-08, 1.6D-01, r^2= 6.2D-01 MO Center= 1.9D-03, 2.3D-03, -3.0D-03, r^2= 6.1D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
15 1.008815 1 O dzz 13 -0.580616 1 O dyy 11 1.727083 1 O dxy
10 -0.366779 1 O dxx 6 -0.227333 1 O s
Vector 15 Occ=0.000000D+00 E= 2.033720D+00 Vector 15 Occ=0.000000D+00 E= 2.033369D+00
MO Center= -5.0D-08, 6.6D-08, 1.2D-01, r^2= 6.1D-01 MO Center= 3.4D-03, 3.4D-03, 4.3D-02, r^2= 6.2D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ --------------- ----- ------------ --------------- ----- ------------ ---------------
11 1.732051 1 O dxy 15 1.012642 1 O dzz 13 -0.512441 1 O dyy
10 -0.438481 1 O dxx 6 -0.226567 1 O s
center of mass center of mass
-------------- --------------
x = 0.00000000 y = 0.00000000 z = 0.09751017 x = -0.00000001 y = -0.00000003 z = -0.12388979
moments of inertia (a.u.) moments of inertia (a.u.)
------------------ ------------------
6.315433940446 0.000000000000 0.000000000000 6.378705068992 0.153373998471 -0.069687034145
0.000000000000 2.193636332720 0.000000000000 0.153373998471 2.014476065716 0.150739744400
0.000000000000 0.000000000000 4.121797607726 -0.069687034145 0.150739744400 4.379134195179
Mulliken analysis of the total density Mulliken analysis of the total density
-------------------------------------- --------------------------------------
Atom Charge Shell Charges Atom Charge Shell Charges
----------- ------ ------------------------------------------------------- ----------- ------ -------------------------------------------------------
1 O 8 8.87 2.00 0.90 2.90 0.92 2.07 0.08 1 O 8 8.87 2.00 0.90 2.90 0.92 2.08 0.08
2 H 1 0.57 0.46 0.10 2 H 1 0.56 0.46 0.11
3 H 1 0.57 0.46 0.10 3 H 1 0.56 0.47 0.10
Multipole analysis of the density wrt the origin Multipole analysis of the density wrt the origin
------------------------------------------------ ------------------------------------------------
L x y z total open nuclear L x y z total open nuclear
- - - - ----- ---- ------- - - - - ----- ---- -------
0 0 0 0 0.000000 0.000000 10.000000 0 0 0 0 -0.000000 0.000000 10.000000
1 1 0 0 -0.000002 0.000000 0.000000 1 1 0 0 -0.026417 0.000000 -0.029313
1 0 1 0 0.000001 0.000000 0.000000 1 0 1 0 -0.023604 0.000000 -0.018537
1 0 0 1 -0.875296 0.000000 0.000000 1 0 0 1 -0.846090 0.000000 -2.169670
2 2 0 0 -5.372336 0.000000 0.000000 2 2 0 0 -5.373227 0.000000 0.007286
2 1 1 0 -0.000002 0.000000 0.000000 2 1 1 0 -0.085617 0.000000 -0.152252
2 1 0 1 0.000001 0.000000 0.000000 2 1 0 1 0.038215 0.000000 0.069311
2 0 2 0 -3.071804 0.000000 4.089795 2 0 2 0 -2.927589 0.000000 4.337695
2 0 1 1 0.000000 0.000000 0.000000 2 0 1 1 -0.071410 0.000000 -0.149465
2 0 0 2 -4.444596 0.000000 1.960717 2 0 0 2 -4.159949 0.000000 2.265483
Parallel integral file used 1 records with 0 large values Parallel integral file used 1 records with 0 large values
@ -535,19 +539,19 @@ task scf gradient
atom coordinates gradient atom coordinates gradient
x y z x y z x y z x y z
1 O 0.000000 0.000000 0.221400 0.000001 0.000000 0.014490 1 O 0.003724 0.002355 -0.005632 0.000909 -0.019294 0.007866
2 H 0.000000 1.429999 -0.885600 -0.000001 0.007296 -0.007245 2 H -0.081649 1.453885 -1.126502 -0.001242 0.025549 -0.011605
3 H 0.000000 -1.429999 -0.885600 -0.000000 -0.007296 -0.007245 3 H 0.022541 -1.491264 -0.998110 0.000333 -0.006255 0.003739
---------------------------------------- ----------------------------------------
| Time | 1-e(secs) | 2-e(secs) | | Time | 1-e(secs) | 2-e(secs) |
---------------------------------------- ----------------------------------------
| CPU | 0.00 | 0.07 | | CPU | 0.00 | 0.03 |
---------------------------------------- ----------------------------------------
| WALL | 0.00 | 0.03 | | WALL | 0.00 | 0.03 |
---------------------------------------- ----------------------------------------
Task times cpu: 0.2s wall: 0.1s Task times cpu: 0.1s wall: 0.1s
NWChem Input Module NWChem Input Module
@ -564,9 +568,9 @@ task scf gradient
------------------------------ ------------------------------
create destroy get put acc scatter gather read&inc create destroy get put acc scatter gather read&inc
calls: 225 225 3182 894 878 0 0 68 calls: 182 182 2869 728 468 0 0 68
number of processes/call 1.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00 number of processes/call 1.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00
bytes total: 8.62e+05 5.44e+05 1.23e+05 0.00e+00 0.00e+00 5.44e+02 bytes total: 6.18e+05 3.56e+05 1.04e+05 0.00e+00 0.00e+00 5.44e+02
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
Max memory consumed for GA by this process: 39432 bytes Max memory consumed for GA by this process: 39432 bytes
@ -619,4 +623,4 @@ MA usage statistics:
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone, T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang. M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
Total times cpu: 0.2s wall: 0.1s Total times cpu: 0.1s wall: 0.2s

626
examples/COUPLE/lammps_nwchem/ao_basis/nwchem_lammps.out.h2o.min.31Jan20 Normal file
View File

@ -0,0 +1,626 @@
argument 1 = nwchem_lammps.nw
============================== echo of input deck ==============================
echo
memory global 40 mb stack 23 mb heap 5 mb
geometry units angstrom noautosym nocenter
O -0.00836667 0.0010006 0.0866404
H 0.0968795 0.837453 -0.346117
H 0.0114839 -0.638453 -0.612122
end
scf
vectors input nwchem_lammps.movecs
end
dft
vectors input nwchem_lammps.movecs
end
basis
O library 6-31g*
H library 6-31g*
end
scf
maxiter 100
end
#dft
# xc b3lyp
#end
task scf gradient
#task dft gradient
================================================================================
Northwest Computational Chemistry Package (NWChem) 6.8
------------------------------------------------------
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352
Copyright (c) 1994-2018
Pacific Northwest National Laboratory
Battelle Memorial Institute
NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file
ACKNOWLEDGMENT
--------------
This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.
Job information
---------------
hostname = almondjoy
program = /home/jboschen/nwchem-6.8.1-release/bin/LINUX64/nwchem
date = Fri Jan 31 00:33:40 2020
compiled = Tue_Oct_01_13:20:43_2019
source = /home/jboschen/nwchem-6.8.1-release
nwchem branch = Development
nwchem revision = N/A
ga revision = 5.6.5
use scalapack = F
input = nwchem_lammps.nw
prefix = nwchem_lammps.
data base = ./nwchem_lammps.db
status = restart
nproc = 1
time left = -1s
Memory information
------------------
heap = 655358 doubles = 5.0 Mbytes
stack = 3014651 doubles = 23.0 Mbytes
global = 5242880 doubles = 40.0 Mbytes (distinct from heap & stack)
total = 8912889 doubles = 68.0 Mbytes
verify = yes
hardfail = no
Directory information
---------------------
0 permanent = .
0 scratch = .
Previous task information
-------------------------
Theory = scf
Operation = gradient
Status = ok
Qmmm = F
Ignore = F
Geometries in the database
--------------------------
Name Natoms Last Modified
-------------------------------- ------ ------------------------
1 geometry 3 Fri Jan 31 00:33:40 2020
The geometry named "geometry" is the default for restart
Basis sets in the database
--------------------------
Name Natoms Last Modified
-------------------------------- ------ ------------------------
1 ao basis 2 Fri Jan 31 00:33:40 2020
The basis set named "ao basis" is the default AO basis for restart
NWChem Input Module
-------------------
Scaling coordinates for geometry "geometry" by 1.889725989
(inverse scale = 0.529177249)
------
auto-z
------
no constraints, skipping 0.0000000000000000
no constraints, skipping 0.0000000000000000
Geometry "geometry" -> ""
-------------------------
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 O 8.0000 -0.00836667 0.00100060 0.08664040
2 H 1.0000 0.09687950 0.83745300 -0.34611700
3 H 1.0000 0.01148390 -0.63845300 -0.61212200
Atomic Mass
-----------
O 15.994910
H 1.007825
Effective nuclear repulsion energy (a.u.) 9.2881144400
Nuclear Dipole moment (a.u.)
----------------------------
X Y Z
---------------- ---------------- ----------------
0.0782914233 0.3911823503 -0.5009962172
Z-matrix (autoz)
--------
Units are Angstrom for bonds and degrees for angles
Type Name I J K L M Value
----------- -------- ----- ----- ----- ----- ----- ----------
1 Stretch 1 2 0.94763
2 Stretch 1 3 0.94740
3 Bend 2 1 3 104.86952
XYZ format geometry
-------------------
3
geometry
O -0.00836667 0.00100060 0.08664040
H 0.09687950 0.83745300 -0.34611700
H 0.01148390 -0.63845300 -0.61212200
==============================================================================
internuclear distances
------------------------------------------------------------------------------
center one | center two | atomic units | angstroms
------------------------------------------------------------------------------
2 H | 1 O | 1.79077 | 0.94763
3 H | 1 O | 1.79032 | 0.94740
------------------------------------------------------------------------------
number of included internuclear distances: 2
==============================================================================
==============================================================================
internuclear angles
------------------------------------------------------------------------------
center 1 | center 2 | center 3 | degrees
------------------------------------------------------------------------------
2 H | 1 O | 3 H | 104.87
------------------------------------------------------------------------------
number of included internuclear angles: 1
==============================================================================
Basis "ao basis" -> "" (cartesian)
-----
O (Oxygen)
----------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 5.48467170E+03 0.001831
1 S 8.25234950E+02 0.013950
1 S 1.88046960E+02 0.068445
1 S 5.29645000E+01 0.232714
1 S 1.68975700E+01 0.470193
1 S 5.79963530E+00 0.358521
2 S 1.55396160E+01 -0.110778
2 S 3.59993360E+00 -0.148026
2 S 1.01376180E+00 1.130767
3 P 1.55396160E+01 0.070874
3 P 3.59993360E+00 0.339753
3 P 1.01376180E+00 0.727159
4 S 2.70005800E-01 1.000000
5 P 2.70005800E-01 1.000000
6 D 8.00000000E-01 1.000000
H (Hydrogen)
------------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 1.87311370E+01 0.033495
1 S 2.82539370E+00 0.234727
1 S 6.40121700E-01 0.813757
2 S 1.61277800E-01 1.000000
Summary of "ao basis" -> "" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
O 6-31g* 6 15 3s2p1d
H 6-31g* 2 2 2s
NWChem SCF Module
-----------------
ao basis = "ao basis"
functions = 19
atoms = 3
closed shells = 5
open shells = 0
charge = 0.00
wavefunction = RHF
input vectors = ./nwchem_lammps.movecs
output vectors = ./nwchem_lammps.movecs
use symmetry = F
symmetry adapt = F
Summary of "ao basis" -> "ao basis" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
O 6-31g* 6 15 3s2p1d
H 6-31g* 2 2 2s
Forming initial guess at 0.0s
Loading old vectors from job with title :
Starting SCF solution at 0.0s
----------------------------------------------
Quadratically convergent ROHF
Convergence threshold : 1.000E-04
Maximum no. of iterations : 100
Final Fock-matrix accuracy: 1.000E-07
----------------------------------------------
#quartets = 1.540D+03 #integrals = 1.424D+04 #direct = 0.0% #cached =100.0%
Integral file = ./nwchem_lammps.aoints.0
Record size in doubles = 65536 No. of integs per rec = 43688
Max. records in memory = 2 Max. records in file = 1392051
No. of bits per label = 8 No. of bits per value = 64
iter energy gnorm gmax time
----- ------------------- --------- --------- --------
1 -76.0107350035 4.75D-05 2.49D-05 0.1
Final RHF results
------------------
Total SCF energy = -76.010735003510
One-electron energy = -123.220958992568
Two-electron energy = 37.922109549024
Nuclear repulsion energy = 9.288114440035
Time for solution = 0.0s
Final eigenvalues
-----------------
1
1 -20.5583
2 -1.3466
3 -0.7130
4 -0.5721
5 -0.4985
6 0.2129
7 0.3068
8 1.0286
9 1.1338
10 1.1678
11 1.1807
12 1.3845
13 1.4334
14 2.0187
15 2.0311
ROHF Final Molecular Orbital Analysis
-------------------------------------
Vector 2 Occ=2.000000D+00 E=-1.346587D+00
MO Center= 1.1D-02, 3.1D-02, -8.5D-02, r^2= 5.0D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
2 0.475648 1 O s 6 0.435095 1 O s
1 -0.209463 1 O s
Vector 3 Occ=2.000000D+00 E=-7.129747D-01
MO Center= 1.5D-02, 3.8D-02, -1.3D-01, r^2= 7.6D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
4 0.500246 1 O py 8 0.299047 1 O py
16 0.232138 2 H s 18 -0.232195 3 H s
Vector 4 Occ=2.000000D+00 E=-5.720760D-01
MO Center= -1.5D-02, -9.7D-03, 1.5D-01, r^2= 6.8D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
5 0.545527 1 O pz 9 0.395332 1 O pz
6 0.326735 1 O s 2 0.164593 1 O s
Vector 5 Occ=2.000000D+00 E=-4.984552D-01
MO Center= -6.2D-03, 4.4D-03, 6.7D-02, r^2= 6.0D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
3 0.634559 1 O px 7 0.507891 1 O px
Vector 6 Occ=0.000000D+00 E= 2.128732D-01
MO Center= 7.5D-02, 1.3D-01, -6.6D-01, r^2= 2.6D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
6 1.437795 1 O s 17 -1.050892 2 H s
19 -1.050374 3 H s 9 -0.494696 1 O pz
5 -0.208359 1 O pz
Vector 7 Occ=0.000000D+00 E= 3.067764D-01
MO Center= 7.1D-02, 1.3D-01, -6.3D-01, r^2= 2.7D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
17 1.413885 2 H s 19 -1.414835 3 H s
8 -0.824411 1 O py 4 -0.320355 1 O py
Vector 8 Occ=0.000000D+00 E= 1.028607D+00
MO Center= 7.1D-03, 2.6D-02, -5.2D-02, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
16 0.839269 2 H s 18 -0.838060 3 H s
8 -0.692349 1 O py 17 -0.426291 2 H s
19 0.425092 3 H s 14 -0.319117 1 O dyz
Vector 9 Occ=0.000000D+00 E= 1.133833D+00
MO Center= -2.7D-02, -2.9D-02, 2.6D-01, r^2= 1.5D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
6 1.621086 1 O s 2 -0.910150 1 O s
9 0.744864 1 O pz 16 0.490586 2 H s
18 0.491102 3 H s 5 -0.484186 1 O pz
17 -0.426087 2 H s 19 -0.425823 3 H s
10 -0.375325 1 O dxx 15 -0.317874 1 O dzz
Vector 10 Occ=0.000000D+00 E= 1.167849D+00
MO Center= -8.0D-03, 1.6D-03, 8.3D-02, r^2= 1.1D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
7 -1.028149 1 O px 3 0.955686 1 O px
Vector 11 Occ=0.000000D+00 E= 1.180721D+00
MO Center= 1.8D-02, 4.2D-02, -1.5D-01, r^2= 1.1D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
16 0.710073 2 H s 18 0.711177 3 H s
5 0.704677 1 O pz 17 -0.389719 2 H s
19 -0.389376 3 H s 6 -0.326170 1 O s
9 -0.288739 1 O pz 13 0.229749 1 O dyy
Vector 12 Occ=0.000000D+00 E= 1.384514D+00
MO Center= -7.4D-04, 1.3D-02, 1.8D-02, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
8 1.510506 1 O py 4 -1.021750 1 O py
17 -0.934844 2 H s 19 0.935260 3 H s
9 0.272171 1 O pz 5 -0.184286 1 O pz
Vector 13 Occ=0.000000D+00 E= 1.433397D+00
MO Center= 4.7D-02, 8.7D-02, -4.1D-01, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
6 3.628985 1 O s 2 -1.436467 1 O s
9 -1.143870 1 O pz 17 -0.805578 2 H s
19 -0.806493 3 H s 13 -0.635948 1 O dyy
5 0.489050 1 O pz 15 -0.410417 1 O dzz
16 -0.312860 2 H s 18 -0.312722 3 H s
Vector 14 Occ=0.000000D+00 E= 2.018721D+00
MO Center= -1.4D-02, -7.1D-03, 1.3D-01, r^2= 6.2D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
15 0.947149 1 O dzz 14 -0.531399 1 O dyz
13 -0.526961 1 O dyy 10 -0.358371 1 O dxx
12 -0.297495 1 O dxz 6 -0.233087 1 O s
Vector 15 Occ=0.000000D+00 E= 2.031133D+00
MO Center= -8.4D-03, 1.0D-03, 8.7D-02, r^2= 6.1D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
11 1.681563 1 O dxy 12 0.314688 1 O dxz
center of mass
--------------
x = -0.00258245 y = 0.02272235 z = 0.04407491
moments of inertia (a.u.)
------------------
6.155330507195 -0.266185800841 0.185335033231
-0.266185800841 2.211585220634 -0.350250164177
0.185335033231 -0.350250164177 4.020009073007
Mulliken analysis of the total density
--------------------------------------
Atom Charge Shell Charges
----------- ------ -------------------------------------------------------
1 O 8 8.87 2.00 0.90 2.91 0.91 2.06 0.08
2 H 1 0.57 0.47 0.10
3 H 1 0.57 0.47 0.10
Multipole analysis of the density wrt the origin
------------------------------------------------
L x y z total open nuclear
- - - - ----- ---- -------
0 0 0 0 -0.000000 0.000000 10.000000
1 1 0 0 0.094145 0.000000 0.078291
1 0 1 0 0.148179 0.000000 0.391182
1 0 0 1 -0.851621 0.000000 -0.500996
2 2 0 0 -5.338111 0.000000 0.035987
2 1 1 0 0.149191 0.000000 0.263306
2 1 0 1 -0.084723 0.000000 -0.165556
2 0 2 0 -3.114464 0.000000 3.960160
2 0 1 1 0.205130 0.000000 0.362991
2 0 0 2 -4.329185 0.000000 1.980308
Parallel integral file used 1 records with 0 large values
NWChem Gradients Module
-----------------------
wavefunction = RHF
RHF ENERGY GRADIENTS
atom coordinates gradient
x y z x y z
1 O -0.015811 0.001891 0.163727 -0.000201 -0.000505 0.001671
2 H 0.183076 1.582557 -0.654066 0.000065 -0.000505 -0.001056
3 H 0.021701 -1.206501 -1.156743 0.000136 0.001011 -0.000616
----------------------------------------
| Time | 1-e(secs) | 2-e(secs) |
----------------------------------------
| CPU | 0.00 | 0.03 |
----------------------------------------
| WALL | 0.00 | 0.03 |
----------------------------------------
Task times cpu: 0.1s wall: 0.1s
NWChem Input Module
-------------------
Summary of allocated global arrays
-----------------------------------
No active global arrays
GA Statistics for process 0
------------------------------
create destroy get put acc scatter gather read&inc
calls: 46 46 2296 477 27 0 0 68
number of processes/call 1.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00
bytes total: 2.70e+05 1.39e+05 2.27e+04 0.00e+00 0.00e+00 5.44e+02
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
Max memory consumed for GA by this process: 37544 bytes
MA_summarize_allocated_blocks: starting scan ...
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
MA usage statistics:
allocation statistics:
heap stack
---- -----
current number of blocks 0 0
maximum number of blocks 18 28
current total bytes 0 0
maximum total bytes 1060104 16000888
maximum total K-bytes 1061 16001
maximum total M-bytes 2 17
CITATION
--------
Please cite the following reference when publishing
results obtained with NWChem:
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
E. Apra, T.L. Windus, W.A. de Jong
"NWChem: a comprehensive and scalable open-source
solution for large scale molecular simulations"
Comput. Phys. Commun. 181, 1477 (2010)
doi:10.1016/j.cpc.2010.04.018
AUTHORS
-------
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
Total times cpu: 0.1s wall: 0.1s

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Sample LAMMPS MD wrapper on NWChem via client/server coupling
See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
Section_howto.html#howto10 for more details on how client/server
coupling works in LAMMPS.
In this dir, the nwchem_wrap.py is a wrapper on the NWChem electronic
structure code so it can work as a "server" code which LAMMPS drives
as a "client" code to perform ab initio MD. LAMMPS performs the MD
timestepping, sends NWChem a current set of coordinates each timestep,
NWChem computes forces and energy (and virial) and returns that info
to LAMMPS.
Messages are exchanged between NWChem and LAMMPS via a client/server
library (CSlib), which is included in the LAMMPS distribution in
lib/message. As explained below you can choose to exchange data
between the two programs either via files or sockets (ZMQ). If the
nwchem_wrap.py program became parallel, or the CSlib library calls were
integrated into NWChem directly, then data could also be exchanged via
MPI.
There are 2 examples provided in the planeware and ao_basis
sub-directories. See details below.
----------------
Build LAMMPS with its MESSAGE package installed:
See the Build extras doc page and its MESSAGE package
section for details.
CMake:
-D PKG_MESSAGE=yes # include the MESSAGE package
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
Traditional make:
cd lammps/lib/message
python Install.py -m -z # build CSlib with MPI and ZMQ support
cd lammps/src
make yes-message
make mpi
You can leave off the -z if you do not have ZMQ on your system.
----------------
Build the CSlib in a form usable by the nwchem_wrapper.py script:
% cd lammps/lib/message/cslib/src
% make shlib # build serial and parallel shared lib with ZMQ support
% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support
This will make a shared library versions of the CSlib, which Python
requires. Python must be able to find both the cslib.py script and
the libcsnompi.so library in your lammps/lib/message/cslib/src
directory. If it is not able to do this, you will get an error when
you run nwchem_wrapper.py.
You can do this by augmenting two environment variables, either from
the command line, or in your shell start-up script. Here is the
sample syntax for the csh or tcsh shells:
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src
----------------
Prepare to use NWChem and the nwchem_wrap.py script
You can run the nwchem_wrap.py script as-is to test that the coupling
between it and LAMMPS is functional. This will use the included
nwchem_lammps.out files output by a previous NWChem run.
But note that the as-is version of nwchem_wrap.py will not attempt to
run NWChem.
To do this, you must edit the 1st nwchemcmd line at the top of
nwchem_wrapper.py to be the launch command needed to run NWChem on
your system. It can be a command to run NWChem in serial or in
parallel, e.g. an mpirun command. Then comment out the 2nd nwchemcmd
line immediately following it.
Ensure you have the necessary NWChem input file in this directory,
suitable for the NWChem calculation you want to perform.
Example input files are provided for both atom-centered AO basis sets
and plane-wave basis sets. Note that the NWChem template file should
be matched to the LAMMPS input script (# of atoms and atom types, box
size, etc).
Once you run NWChem yourself, the nwchem_lammps.out file will be
overwritten.
The syntax of the wrapper is:
nwchem_wrap.py file/zmq ao/pw input_template
* file/zmg = messaging mode, must match LAMMPS messaging mode
* ao/pw = basis set mode, selects between atom-centered and plane-wave
the input_template file must correspond to the appropriate basis set mode:
the "ao" mode supports the scf and dft modules in NWChem,
the "pw" mode supports the nwpw module.
* input_template = NWChem input file used as template, must include a
"geometry" block with the atoms in the simulation, dummy
xyz coordinates should be included (but are not used).
Atom ordering must match LAMMPS input.
During a simulation, the molecular orbitals from the previous timestep
will be used as the initial guess for the next NWChem calculation. If
a file named "nwchem_lammps.movecs" is in the directory the wrapper is
called from, these orbitals will be used as the initial guess orbitals
in the first step of the simulation.
----------------
Example directories
(1) planewave
Demonstrates coupling of the nwpw module in NWChem with LAMMPS. Only fully
periodic boundary conditions and orthogonal simulation boxes are currently
supported by the wrapper. The included files provide an example run using a
2 atom unit cell of tungsten.
Files:
* data.W LAMMPS input with geometry information
* in.client.W LAMMPS simulation input
* log.client.output LAMMPS simulation output
* w.nw NWChem template input file
* nwchem_lammps.out NWChem output
(2) ao_basis
Demonstrates coupling of the scf (or dft) modules in NWChem with
LAMMPS. Only fully aperiodic boundary conditions are currently
supported by the wrapper. The included files provide an example run
using a single water molecule.
Files:
* data.h2o LAMMPS input with geometry information
* in.client.h2o LAMMPS simulation input
* log.client.output LAMMPS simulation output
* h2o.nw NWChem template input file
* nwchem_lammps.out NWChem output
As noted above, you can run the nwchem_wrap.py script as-is to test that
the coupling between it and LAMMPS is functional. This will use the included
nwchem_lammps.out files.
----------------
To run in client/server mode:
NOTE: The nwchem_wrap.py script must be run with Python version 2, not
3. This is because it used the CSlib python wrapper, which only
supports version 2. We plan to upgrade CSlib to support Python 3.
Both the client (LAMMPS) and server (nwchem_wrap.py) must use the same
messaging mode, namely file or zmq. This is an argument to the
nwchem_wrap.py code; it can be selected by setting the "mode" variable
when you run LAMMPS. The default mode = file.
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
package was installed with socket (ZMQ) support. This means either of
the messaging modes can be used and LAMMPS can be run in serial or
parallel. The nwchem_wrap.py code is always run in serial, but it
launches NWChem from Python via an mpirun command which can run NWChem
itself in parallel.
When you run, the server should print out thermodynamic info every
timestep which corresponds to the forces and virial computed by NWChem.
NWChem will also generate output files each timestep. Output files from
previous timesteps are archived in a "nwchem_logs" directory.
The examples below are commands you should use in two different
terminal windows. The order of the two commands (client or server
launch) does not matter. You can run them both in the same window if
you append a "&" character to the first one to run it in the
background.
--------------
File mode of messaging:
% mpirun -np 1 lmp_mpi -v mode file < in.client.W
% python nwchem_wrap.py file pw w.nw
% mpirun -np 2 lmp_mpi -v mode file < in.client.h2o
% python nwchem_wrap.py file ao h2o_dft.nw
ZMQ mode of messaging:
% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W
% python nwchem_wrap.py zmq pw w.nw
% mpirun -np 2 lmp_mpi -v mode zmq < in.client.h2o
% python nwchem_wrap.py zmq ao h2o_dft.nw

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examples/COUPLE/lammps_nwchem/lammps_nwchem/ao_basis/data.h2o
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@ -1,20 +0,0 @@
LAMMPS H2O data file
3 atoms
2 atom types
-10.0 10.0 xlo xhi
-10.0 10.0 ylo yhi
-10.0 10.0 zlo zhi
Masses
1 15.994915008544922
2 1.0078250169754028
Atoms
1 1 0.0 0.0 0.0
2 2 0.0 0.756723 -0.585799
3 2 0.0 -0.756723 -0.585799

25
examples/COUPLE/lammps_nwchem/lammps_nwchem/ao_basis/h2o.nw
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echo
memory global 40 mb stack 23 mb heap 5 mb
geometry units angstrom noautosym
O 0.0 0.0 0.0
H 1.0 0.5 0.0
H -1.0 0.5 0.0
end
basis
O library 6-31g*
H library 6-31g*
end
scf
maxiter 100
end
#dft
# xc b3lyp
#end
task scf gradient
#task dft gradient

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examples/COUPLE/lammps_nwchem/lammps_nwchem/nwchem_wrap.py
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#!/usr/bin/env python
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
# ----------------------------------------------------------------------
# Syntax: nwchem_wrap.py file/zmq ao/pw input_template
# file/zmg = messaging mode, must match LAMMPS messaging mode
# ao/pw = basis set mode, selects between atom-centered and plane-wave
# the input_template file must correspond to the appropriate basis set mode:
# the "ao" mode supports the scf and dft modules in NWChem,
# the "pw" mode supports the nwpw module.
# input_template = NWChem input file used as template, must include a
# "geometry" block with the atoms in the simulation, dummy
# xyz coordinates should be included (but are not used).
# Atom ordering must match LAMMPS input.
# wrapper on NWChem
# receives message with list of coords
# creates NWChem inputs
# invokes NWChem to calculate self-consistent energy of that config
# reads NWChem outputs
# sends message with energy, forces, pressure to client
from __future__ import print_function
import sys
version = sys.version_info[0]
if version == 3:
sys.exit("The CSlib python wrapper does not yet support python 3")
import subprocess
import re
import os
import shutil
from cslib import CSlib
# comment out 2nd line once 1st line is correct for your system
nwchemcmd = "mpirun -np 1 /usr/bin/nwchem nwchem_lammps.nw > "
nwchemcmd = "touch tmp"
# enums matching FixClientMD class in LAMMPS
SETUP,STEP = range(1,2+1)
DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1)
FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1)
# -------------------------------------
# functions
# error message and exit
def error(txt):
print("ERROR:",txt)
sys.exit(1)
# -------------------------------------
# read initial input file to setup problem
# return natoms
def nwchem_setup_ao(input):
template = open(input,'r')
geometry_block = False
natoms = 0
while True:
line = template.readline()
if not line: break
if geometry_block and re.search("end",line):
geometry_block = False
if geometry_block and not re.match("#",line) :
natoms += 1
if re.search("geometry",line):
geometry_block = True
return natoms
# -------------------------------------
# write a new input file for NWChem
# assumes the NWChem input geometry is to be specified in angstroms
def nwchem_input_write_ao(input,coords):
template = open(input,'r')
new_input = open("nwchem_lammps.nw",'w')
geometry_block = False
i = 0
while True:
line = template.readline()
if not line: break
if geometry_block and not re.match("#",line) and re.search("end",line):
geometry_block = False
if os.path.exists("nwchem_lammps.movecs"):
# The below is hacky, but one of these lines will be ignored
# by NWChem depending on if the input file is for scf/dft.
append = "\nscf\n vectors input nwchem_lammps.movecs\nend\n"
append2 = "\ndft\n vectors input nwchem_lammps.movecs\nend\n"
line = line + append + append2
if geometry_block and not re.match("#",line):
x = coords[3*i+0]
y = coords[3*i+1]
z = coords[3*i+2]
coord_string = " %g %g %g \n" % (x,y,z)
atom_string = line.split()[0]
line = atom_string + coord_string
i += 1
if (not re.match("#",line)) and re.search("geometry",line):
geometry_block = True
line = "geometry units angstrom noautosym\n"
print(line,file=new_input,end='')
new_input.close()
# -------------------------------------
# read a NWChem output nwchem_lammps.out file
def nwchem_read_ao(natoms, log):
nwchem_output = open(log, 'r')
energy_pattern = r"Total \w+ energy"
gradient_pattern = "x y z x y z"
eout = 0.0
fout = []
while True:
line = nwchem_output.readline()
if not line: break
# pattern match for energy
if re.search(energy_pattern,line):
eout = float(line.split()[4])
# pattern match for forces
if re.search(gradient_pattern, line):
for i in range(natoms):
line = nwchem_output.readline()
forces = line.split()
fout += [float(forces[5]), float(forces[6]), float(forces[7])]
# convert units
hartree2eV = 27.21138602
bohr2angstrom = 0.52917721092
eout = eout * hartree2eV
fout = [i * hartree2eV/bohr2angstrom for i in fout]
print(eout)
return eout,fout
# -------------------------------------
# read initial planewave input file to setup problem
# return natoms,box
def nwchem_setup_pw(input):
template = open(input,'r')
geometry_block = False
system_block = False
coord_pattern = r"^\s*\w{1,2}(?:\s+-?(?:\d+.?\d*|\d*.?\d+)){3}"
natoms = 0
box = []
while True:
line = template.readline()
if not line: break
if geometry_block and re.search("system crystal",line):
system_block = True
for i in range(3):
line = template.readline()
line = re.sub(r'd|D', 'e', line)
box += [float(line.split()[1])]
if geometry_block and not system_block and re.match("#",line) and re.search("end",line):
geometry_block = False
if system_block and re.search("end",line):
system_block = False
if geometry_block and not re.match("#",line) and re.search(coord_pattern,line):
natoms += 1
if re.search("geometry",line) and not re.match("#",line):
geometry_block = True
return natoms,box
# -------------------------------------
# write a new planewave input file for NWChem
# assumes the NWChem input geometry is to be specified fractional coordinates
def nwchem_input_write_pw(input,coords,box):
template = open(input,'r')
new_input = open("nwchem_lammps.nw",'w')
writing_atoms = False
geometry_block = False
system_block = False
coord_pattern = r"^\s*\w{1,2}(?:\s+-?(?:\d+.?\d*|\d*.?\d+)){3}"
i = 0
while True:
line = template.readline()
if not line: break
if geometry_block and re.search("system crystal",line):
system_block = True
if geometry_block and not system_block and not re.match("#",line) and re.search("end",line):
geometry_block = False
if os.path.exists("nwchem_lammps.movecs"):
append = "\nnwpw\n vectors input nwchem_lammps.movecs\nend\n"
line = line + append
if system_block and re.search("end",line):
system_block = False
if geometry_block and not re.match("#",line) and re.search(coord_pattern,line):
x = coords[3*i+0] / box[0]
y = coords[3*i+1] / box[1]
z = coords[3*i+2] / box[2]
coord_string = " %g %g %g \n" % (x,y,z)
atom_string = line.split()[0]
line = atom_string + coord_string
i += 1
if re.search("geometry",line) and not re.match("#",line):
geometry_block = True
print(line,file=new_input,end='')
new_input.close()
# -------------------------------------
# read a NWChem output nwchem_lammps.out file for planewave calculation
def nwchem_read_pw(log):
nw_output = open(log, 'r')
eout = 0.0
sout = []
fout = []
reading_forces = False
while True:
line = nw_output.readline()
if not line: break
# pattern match for energy
if re.search("PSPW energy",line):
eout = float(line.split()[4])
# pattern match for forces
if re.search("C\.O\.M", line):
reading_forces = False
if reading_forces:
forces = line.split()
fout += [float(forces[3]), float(forces[4]), float(forces[5])]
if re.search("Ion Forces",line):
reading_forces = True
# pattern match for stress
if re.search("=== total gradient ===",line):
stensor = []
for i in range(3):
line = nw_output.readline()
line = line.replace("S ="," ")
stress = line.split()
stensor += [float(stress[1]), float(stress[2]), float(stress[3])]
sxx = stensor[0]
syy = stensor[4]
szz = stensor[8]
sxy = 0.5 * (float(stensor[1]) + float(stensor[3]))
sxz = 0.5 * (stensor[2] + stensor[6])
syz = 0.5 * (stensor[5] + stensor[7])
sout = [sxx,syy,szz,sxy,sxz,syz]
# convert units
hartree2eV = 27.21138602
bohr2angstrom = 0.52917721092
austress2bar = 294210156.97
eout = eout * hartree2eV
fout = [i * hartree2eV/bohr2angstrom for i in fout]
sout = [i * austress2bar for i in sout]
return eout,fout,sout
# -------------------------------------
# main program
# command-line args
#
if len(sys.argv) != 4:
print("Syntax: python nwchem_wrap.py file/zmq ao/pw input_template")
sys.exit(1)
comm_mode = sys.argv[1]
basis_type = sys.argv[2]
input_template = sys.argv[3]
if comm_mode == "file": cs = CSlib(1,comm_mode,"tmp.couple",None)
elif comm_mode == "zmq": cs = CSlib(1,comm_mode,"*:5555",None)
else:
print("Syntax: python nwchem_wrap.py file/zmq")
sys.exit(1)
natoms = 0
box = []
if basis_type == "ao":
natoms = nwchem_setup_ao(input_template)
elif basis_type == "pw":
natoms,box = nwchem_setup_pw(input_template)
# initial message for AIMD protocol
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
if msgID != 0: error("Bad initial client/server handshake")
protocol = cs.unpack_string(1)
if protocol != "md": error("Mismatch in client/server protocol")
cs.send(0,0)
# endless server loop
i = 0
if not os.path.exists("nwchem_logs"):
os.mkdir("nwchem_logs")
while 1:
# recv message from client
# msgID = 0 = all-done message
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
if msgID < 0: break
# SETUP receive at beginning of each run
# required fields: DIM, PERIODICITY, ORIGIN, BOX,
# NATOMS, COORDS
# optional fields: others in enum above, but NWChem ignores them
if msgID == SETUP:
origin = []
box_lmp = []
natoms_recv = ntypes_recv = 0
types = []
coords = []
for field in fieldID:
if field == DIM:
dim = cs.unpack_int(DIM)
if dim != 3: error("NWChem only performs 3d simulations")
elif field == PERIODICITY:
periodicity = cs.unpack(PERIODICITY,1)
if basis_type == "ao":
if periodicity[0] or periodicity[1] or periodicity[2]:
error("NWChem AO basis wrapper only currently supports fully aperiodic systems")
elif basis_type == "pw":
if not periodicity[0] or not periodicity[1] or not periodicity[2]:
error("NWChem PW basis wrapper only currently supports fully periodic systems")
elif field == ORIGIN:
origin = cs.unpack(ORIGIN,1)
elif field == BOX:
box_lmp = cs.unpack(BOX,1)
if (basis_type == "pw"):
if (box[0] != box_lmp[0] or box[1] != box_lmp[4] or box[2] != box_lmp[8]):
error("NWChem wrapper mismatch in box dimensions")
elif field == NATOMS:
natoms_recv = cs.unpack_int(NATOMS)
if natoms != natoms_recv:
error("NWChem wrapper mismatch in number of atoms")
elif field == COORDS:
coords = cs.unpack(COORDS,1)
if not origin or not box_lmp or not natoms or not coords:
error("Required NWChem wrapper setup field not received");
# STEP receive at each timestep of run or minimization
# required fields: COORDS
# optional fields: ORIGIN, BOX
elif msgID == STEP:
coords = []
for field in fieldID:
if field == COORDS:
coords = cs.unpack(COORDS,1)
if not coords: error("Required NWChem wrapper step field not received");
else: error("NWChem wrapper received unrecognized message")
# unpack coords from client
# create NWChem input
if basis_type == "ao":
nwchem_input_write_ao(input_template,coords)
elif basis_type == "pw":
nwchem_input_write_pw(input_template,coords,box)
# invoke NWChem
i += 1
log = "nwchem_lammps.out"
archive = "nwchem_logs/nwchem_lammps" + str(i) + ".out"
cmd = nwchemcmd + log
print("\nLaunching NWChem ...")
print(cmd)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
shutil.copyfile(log,archive)
# process NWChem output
if basis_type == "ao":
energy,forces = nwchem_read_ao(natoms,log)
virial = [0,0,0,0,0,0]
elif basis_type == "pw":
energy,forces,virial = nwchem_read_pw(log)
# return forces, energy to client
cs.send(msgID,3)
cs.pack(FORCES,4,3*natoms,forces)
cs.pack_double(ENERGY,energy)
cs.pack(VIRIAL,4,6,virial)
# final reply to client
cs.send(0,0)
# clean-up
del cs

15
examples/COUPLE/lammps_nwchem/lammps_nwchem/planewave/data.W
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@ -1,15 +0,0 @@
LAMMPS W data file
2 atoms
1 atom types
0.0 3.16 xlo xhi
0.0 3.16 ylo yhi
0.0 3.16 zlo zhi
Atoms
1 1 0.000 0.000 0.000
2 1 1.58 1.58 1.58

34
examples/COUPLE/lammps_nwchem/lammps_nwchem/planewave/in.client.W
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@ -1,34 +0,0 @@
# small W unit cell for use with NWChem
variable mode index file
if "${mode} == file" then &
"message client md file tmp.couple" &
elif "${mode} == zmq" &
"message client md zmq localhost:5555" &
variable x index 1
variable y index 1
variable z index 1
units metal
atom_style atomic
atom_modify sort 0 0.0 map yes
read_data data.W
mass 1 183.85
replicate $x $y $z
velocity all create 300.0 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 10 check no
fix 1 all nve
fix 2 all client/md
fix_modify 2 energy yes
thermo 1
run 3

76
examples/COUPLE/lammps_nwchem/lammps_nwchem/planewave/log.client.output
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LAMMPS (18 Sep 2018)
# small W unit cell for use with NWChem
variable mode index file
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
message client md file tmp.couple
variable x index 1
variable y index 1
variable z index 1
units metal
atom_style atomic
atom_modify sort 0 0.0 map yes
read_data data.W
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
mass 1 183.85
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
1 by 1 by 1 MPI processor grid
2 atoms
Time spent = 0.000187325 secs
velocity all create 300.0 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 10 check no
fix 1 all nve
fix 2 all client/md
fix_modify 2 energy yes
thermo 1
run 3
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 -549.75686 36815830
1 300 0 0 -549.75686 36815830
2 300 0 0 -549.75686 36815830
3 300 0 0 -549.75686 36815830
Loop time of 0.400933 on 1 procs for 3 steps with 2 atoms
Performance: 0.646 ns/day, 37.123 hours/ns, 7.483 timesteps/s
0.1% CPU use with 1 MPI tasks x 1 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 | 4.755e-06 | 4.755e-06 | 4.755e-06 | 0.0 | 0.00
Output | 0.00010114 | 0.00010114 | 0.00010114 | 0.0 | 0.03
Modify | 0.40082 | 0.40082 | 0.40082 | 0.0 | 99.97
Other | | 1.232e-05 | | | 0.00
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7 ave 7 max 7 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 not checked
Total wall time: 0:00:09

2305
examples/COUPLE/lammps_nwchem/lammps_nwchem/planewave/nwchem_lammps.out
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File diff suppressed because it is too large Load Diff

28
examples/COUPLE/lammps_nwchem/lammps_nwchem/planewave/w.nw
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@ -1,28 +0,0 @@
echo
#**** Enter the geometry using fractional coordinates ****
geometry units angstrom noautosym
system crystal
lat_a 3.16d0
lat_b 3.16d0
lat_c 3.16d0
end
W 0.0 0.0 0.0
W 0.5 0.5 0.5
end
#***** setup the nwpw gamma point code ****
nwpw
simulation_cell
ngrid 16 16 16
end
ewald_ncut 8
mulliken
lcao #old default
end
nwpw
tolerances 1.0d-9 1.0d-9
end
task pspw stress

4
examples/COUPLE/lammps_nwchem/nwchem_wrap.py
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@ -117,7 +117,7 @@ def nwchem_input_write_ao(input,coords):
if (not re.match("#",line)) and re.search("geometry",line): if (not re.match("#",line)) and re.search("geometry",line):
geometry_block = True geometry_block = True
line = "geometry units angstrom noautosym\n" line = "geometry units angstrom noautosym nocenter\n"
print(line,file=new_input,end='') print(line,file=new_input,end='')
@ -154,7 +154,7 @@ def nwchem_read_ao(natoms, log):
hartree2eV = 27.21138602 hartree2eV = 27.21138602
bohr2angstrom = 0.52917721092 bohr2angstrom = 0.52917721092
eout = eout * hartree2eV eout = eout * hartree2eV
fout = [i * hartree2eV/bohr2angstrom for i in fout] fout = [i * -hartree2eV/bohr2angstrom for i in fout]
return eout,fout return eout,fout