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more examples in QUANTUM/LATTE

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This commit is contained in:
Steve Plimpton
2023-02-08 12:48:50 -07:00
parent 3419bfa3f2
commit 10b20ec647
40 changed files with 2327 additions and 255 deletions
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120
examples/QUANTUM/LATTE/README
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@ -10,35 +10,34 @@ Step 4: run the water AIMD problem for a few steps
Step 1: build LAMMPS
The molecule and kspace packages are needed for the 2-water test
problem. Copy the final LAMMPS executable into the
examples/QUANTUM/PySCF directory.
The molecule package is needed. Copy the final LAMMPS executable into
the examples/QUANTUM/LATTE directory.
Traditional make:
% cd ~/lammps/lib/mdi
% python Install.py -m mpi
% cd ~/lammps/src
% make yes-mdi yes-molecule yes-kspace
% make yes-mdi yes-molecule
% make -j mpi
% cp lmp_mpi ~/lammps/examples/QUANTUM/PySCF
% cp lmp_mpi ~/lammps/examples/QUANTUM/LATTE
CMake:
% cd ~/lammps
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes -D PKG_KSPACE=yes ../cmake
% cmake -DPKG_MDI=yes -DPKG_MOLECULE=yes ../cmake
% make -j
% cp lmp ~/lammps/examples/QUANTUM/PySCF/lmp_mpi
% cp lmp ~/lammps/examples/QUANTUM/LATTE/lmp_mpi
---------------------------------
---------------------------------
Step 2: install the MDI code coupling package
Step 2: download/build MDI code coupling package
(a) grab the MDI Git repo
(a) clone the MDI Git repo
% mkdir git; cd mdi
% mkdir mdi; cd mdi
% git clone git@github.com:MolSSI-MDI/MDI_Library.git git
(b) build MDI
@ -48,8 +47,8 @@ Step 2: install the MDI code coupling package
% cmake ..
% make -j
(c) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find MDI:
(c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that
Python can find MDI:
For bash:
@ -66,91 +65,84 @@ For (t)csh:
Step 3: download/build LATTE
(a) download/build LATTE on your box
(a) clone the skimLATTE repo
NOTE: add instructions here
% mkdir latte; cd latte
% git clone git@github.com:lanl/LATTE.git git
(b) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find PySCF:
(b) build LATTE as a shared library
% cd ~/latte/git
% mkdir build; cd build
% cmake -DBUILD_SHARED_LIBS=on ../cmake
% make
(c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that
the liblatte.so file can be found:
For bash:
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/pyscf/git"
% export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/home/sjplimp/latte/git/build"
% hash -r
For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/pyscf/git
% setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/latte/git/build
% rehash
(c) Check that you can import the 4 Python modules which the script
that wraps PySCF will need:
% python
>>> import numpy as np
>>> from mpi4py import MPI
>>> import MDI_Library as mdi
>>> import pyscf
---------------------------------
---------------------------------
Step 4: run the water AIMD problem for a few steps
Step 4: perform test runs in any of 3 modes
% cd ~/lammps/examples/QUANTUM/LATTE
These tests are in lammps/examples/QUANTUM/LATTE
# Run with TCP: 1 proc each
in.ch4 = AIMD with CH4 molecule
in.graphene = AIMD with graphene
in.series = series of 3 UO2 conformations
in.sucrose = AIMD of sucrose molecule
in.uo2 = two molecules of UO2
in.water = eight water molecules
% lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.tcp.1 -in in.water &
** run 2 executables with TCP/IP, 1 proc each
% python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.water
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.tcp.1 -in in.water &
python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.water
# Run with MPI: 1 proc each
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.uo2.tcp.1 -in in.uo2 &
python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.uo2
% mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.mpi.1 -in in.water : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.water
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.series.tcp.1 -in in.series &
python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.uo2
# Run in plugin mode: 1 proc
** run 2 executables with MPI, 1 proc each
% lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.water.plugin.1 -in in.water.plugin
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.mpi.1 -in in.water : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.water
---------------------------------
---------------------------------
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.min.mpi.1 -in in.water.min : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.generic
Step 5: run the UO2 AIMD problem for a few steps
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.uo2.mpi.1 -in in.uo2 : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.uo2
% cd ~/lammps/examples/QUANTUM/LATTE
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.ch4.mpi.1 -in in.ch4 : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.generic
# Run with TCP: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.sucrose.mpi.1 -in in.sucrose : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.generic
% lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.uo2.tcp.1 -in in.uo2 &
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.graphene.mpi.1 -in in.graphene : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.generic
% python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.uo2
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.series.mpi.1 -in in.series : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.uo2
# Run with MPI: 1 proc each
** run LATTE as plugin MDI engine, on 1 proc
% mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.uo2.mpi.1 -in in.uo2 : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.uo2
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.water.plugin.1 -in in.water.plugin
# Run in plugin mode: 1 proc
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.water.min.plugin.1 -in in.water.min.plugin
% lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.uo2.plugin.1 -in in.uo2.plugin
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.uo2.plugin.1 -in in.uo2.plugin
---------------------------------
---------------------------------
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.ch4.plugin.1 -in in.ch4.plugin
Step 6: run the UO2 series problem
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.sucrose.plugin.1 -in in.sucrose.plugin
% cd ~/lammps/examples/QUANTUM/LATTE
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.graphene.plugin.1 -in in.graphene.plugin
# Run with TCP: 1 proc each
% lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.series.tcp.1 -in in.series &
% python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.uo2
# Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.series.mpi.1 -in in.series : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.uo2
# Run in plugin mode: 1 proc
% lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.series.plugin.1 -in in.series.plugin
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.series.plugin.1 -in in.series.plugin

179
examples/QUANTUM/LATTE/README.old
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@ -1,179 +0,0 @@
LATTE is a semi-empirical tight-binding quantum code, developed
primarily at Los Alamos National Labs.
See these links:
https://www.osti.gov/biblio/1526907-los-alamos-transferable-tight-binding-energetics-latte-version
https://github.com/lanl/LATTE
LAMMPS has 2 ways of working with LATTE:
(1) Via its LATTE package and the fix latte command
must run LAMMPS on a single processor, it calls LATTE as a library
(2) Via its MDI package and the code-coupling MDI library
(a) can run LAMMPS and LATTE as stand-alone codes
LAMMPS can be run on any number of procs
LATTE must run on a single proc, but can use OpenMP
(b) can run LAMMPS with LATTE as a plug-in library
must run LAMMPS on a single processor
Examples for use case (1) are in the examples/latte dir. Use case (2)
is illustrated in this dir.
NOTE: If you compare MDI runs in this dir to similar fix latte runs in
examples/latte, the answers for energy and virial will be differnt.
This is b/c the version of LATTE used by the fix latte command within
the LATTE package is older than the version of LATTE used here.
------------------
Building 3 codes needed to run these examples
(1) Download and build MDI
% git clone git@github.com:MolSSI-MDI/MDI_Library.git mdi
% cd mdi
% mkdir build; cd build
% cmake .. # includes support for all langauges (incl Fortran, Python)
% make
(2) Download and build LATTE with MDI support
% git clone git@github.com:lanl/LATTE.git latte
% cd latte
% git checkout skimLATTE-progress # goto branch with MDI support
% cp makefiles/makefile.CHOICES.mdi makefile.CHOICES # so can now edit
% edit makefile.CHOICES settings to have these settings:
MAKELIB = OFF, SHARED = ON, MDI = ON
MDI_PATH must point to CMake build of MDI in (1),
e.g. /home/sjplimp/mdi/build/MDI_Library
comment out 2 LIB lines with CUDA-CUDART_LIBRARY
% make clean
% make # creates liblatte.so and LATTE_DOUBLE with support for MDI
(3) Build LAMMPS with its MDI package
also with the MOLECULE package for these example scripts
Build with traditional make
% cd lammps/lib/mdi
% python Install.py -m mpi # downloads and builds MDI
% cd ../../src
% make yes-mdi yes-molecule
$ make mpi # creates lmp_mpi
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
% make # creates lmp
Build with CMake
% cd lammps
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
% make # creates lmp
(4) Copy LAMMPS and LATTE executables into this dir
Copy the LAMMPS executable (lmp_mpi or lmp) into this dir as lmp_mpi.
Copy the LATTE executable LATTE_DOUBLE into this dir.
The run commands below assume you have done this.
(5) Ensure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
with its libmdi.so file, e.g. mdi/build/MDI_Library. This is needed
so when LATTE_DOUBLE runs as an executable it will able to find
libmdi.so.
------------------
Notes on LATTE usage
You must run this version of LATTE on a single MPI processor.
However, you can use OpenMP with LATTE. To do this you need to build
LATTE with OpenMP support by editing the makefile.CHOICES file to
include -fopenmp with FFLAGS and LINKFLAGS. Also -lapack and -lblas
need to be added to LIB, and those libraries must be available on your
system. For best performance you should also build LATTE with its
PROGRESS and BML libraries. Building those libs is more complex,
see details here:
https://github.com/lanl/LATTE_SUPER/tree/allMachines/Laptop
At run time, you need to also first set an environment variable for
the number of OpenMP threads to use, e.g.
% export OMP_NUM_THREADS=12
By default LATTE reads the latte.in file for its parameters. That
file specifies other files LATTE will read. With MDI, the driver code
(e.g. LAMMPS) can use the >FNAME command to specify an alternate
filename to use instead of latte.in.
By default LATTE writes out a log.latte file with info about its
calculations. An "OUTFILE= logfile" setting in latte.in can rename
this file.
---------
Run example #1: AIMD
* Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.water -log log.water.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.water -log log.water.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run in plugin mode: 1 proc
lmp_mpi -mdi \
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
-in in.water.plugin -log log.water.lammps.plugin
NOTE: The -plugin_path needs to point to where LATTE was built in step
(2).
---------
Run example #2: AIMD
* Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.aimd -log log.aimd.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.aimd -log log.aimd.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run in plugin mode: 1 proc
lmp_mpi -mdi \
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
-in in.aimd.plugin -log log.aimd.lammps.plugin
---------
Run example #3: sequence of configurations
* Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.series -log log.series.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.series -log log.series.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run in plugin mode: 1 proc
lmp_mpi -mdi \
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
-in in.series.plugin -log log.series.lammps.plugin

36
examples/QUANTUM/LATTE/TBparam_generic/bondints.nonortho Normal file
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@ -0,0 +1,36 @@
Noints= 34
Element1 Element2 Kind H0 B1 B2 B3 B4 B5 R1 Rcut H0 B1 B2 B3 B4 B5 R1 Rcut
N O sss -11.430028 -2.257346 -1.152844 0.000000 0.000000 1.200000 3.500000 4.000000 0.340064 -1.703613 -0.622348 0.036738 -0.040158 1.200000 3.500000 4.000000
N O sps 11.597479 -1.382001 -0.765170 0.000000 0.000000 1.200000 3.500000 4.000000 -0.370946 -1.040947 -0.931097 0.252441 -0.115450 1.200000 3.500000 4.000000
O N sps 12.143744 -0.822913 -0.676127 0.000000 0.000000 1.200000 3.500000 4.000000 -0.420014 -1.107918 -0.905594 0.188424 -0.088365 1.200000 3.500000 4.000000
N O pps 9.465191 -1.082032 -0.769214 0.000000 0.000000 1.200000 3.500000 4.000000 -0.314073 0.499050 -2.914288 2.067657 -0.738439 1.200000 3.500000 4.000000
N O ppp -4.676789 -2.171480 -0.288002 0.000000 0.000000 1.200000 3.500000 4.000000 0.223937 -1.991867 -0.537630 -0.081270 -0.004130 1.200000 3.500000 4.000000
C O sss -14.369472 -2.077439 -0.875471 0.000000 0.000000 1.200000 3.500000 4.000000 0.375339 -1.547372 -0.642492 0.020614 -0.026699 1.200000 3.500000 4.000000
C O sps 9.576296 -1.156217 -0.494803 0.000000 0.000000 1.200000 3.500000 4.000000 -0.373027 -0.776043 -1.019920 0.257539 -0.102838 1.200000 3.500000 4.000000
O C sps 14.037374 -1.192632 -0.654572 0.000000 0.000000 1.200000 3.500000 4.000000 -0.458068 -1.035067 -0.937868 0.190562 -0.077841 1.200000 3.500000 4.000000
C O pps 9.331152 -0.718120 -0.822100 0.000000 0.000000 1.200000 3.500000 4.000000 -0.322293 0.795473 -3.476601 2.589965 -0.897800 1.200000 3.500000 4.000000
C O ppp -5.334367 -2.263939 -0.204910 0.000000 0.000000 1.200000 3.500000 4.000000 0.244570 -1.922717 -0.573671 -0.057280 -0.004108 1.200000 3.500000 4.000000
C N sss -7.010061 -1.730597 -0.575559 0.000000 0.000000 1.500000 3.500000 4.000000 0.263438 -1.754525 -0.584215 -0.007801 -0.021729 1.500000 3.500000 4.000000
C N sps 7.543283 -1.293768 -0.624363 0.000000 0.000000 1.500000 3.500000 4.000000 -0.326609 -1.197485 -0.807786 0.134891 -0.084373 1.500000 3.500000 4.000000
N C sps 9.090970 -1.494255 -0.616711 0.000000 0.000000 1.500000 3.500000 4.000000 -0.337943 -1.335442 -0.769693 0.119373 -0.079493 1.500000 3.500000 4.000000
C N pps 6.892240 -0.931920 -0.769164 0.000000 0.000000 1.500000 3.500000 4.000000 -0.350240 -0.467439 -1.849316 1.854403 -0.988471 1.500000 3.500000 4.000000
C N ppp -2.903346 -2.149349 -0.253006 0.000000 0.000000 1.500000 3.500000 4.000000 0.158424 -2.114409 -0.582346 -0.051076 -0.006183 1.500000 3.500000 4.000000
C C sss -9.404207 -1.363297 -0.507128 0.000000 0.000000 1.400000 3.500000 4.000000 0.346977 -1.519820 -0.570812 -0.013518 -0.015829 1.400000 3.500000 4.000000
C C sps 8.662429 -1.047410 -0.661999 0.000000 0.000000 1.400000 3.500000 4.000000 -0.400467 -0.984048 -0.853949 0.157178 -0.073381 1.400000 3.500000 4.000000
C C pps 6.811512 -0.552299 -0.776890 0.000000 0.000000 1.400000 3.500000 4.000000 -0.382417 0.102889 -2.786680 2.646356 -1.134320 1.400000 3.500000 4.000000
C C ppp -3.550127 -1.925572 -0.132715 0.000000 0.000000 1.400000 3.500000 4.000000 0.214357 -1.948923 -0.578323 -0.034356 -0.007257 1.400000 3.500000 4.000000
H C sss -9.072577 -1.393093 -0.430611 0.000000 0.000000 1.100000 3.500000 4.000000 0.416003 -1.459596 -0.654874 0.009140 -0.012658 1.100000 3.500000 4.000000
H C sps 8.176008 -0.985177 -0.427403 0.000000 0.000000 1.100000 3.500000 4.000000 -0.495695 -0.901626 -1.007214 0.189808 -0.057087 1.100000 3.500000 4.000000
H H sss -9.340000 -1.145903 -0.391777 0.000000 0.000000 0.750000 3.500000 4.000000 0.575007 -1.391261 -0.778831 0.080209 -0.017759 0.750000 3.500000 4.000000
O O sss -12.737687 -1.851608 -0.666621 0.000000 0.000000 1.200000 3.500000 4.000000 0.296445 -1.911896 -0.663451 0.038054 -0.046608 1.200000 3.500000 4.000000
O O sps 13.683050 -1.684554 -0.468349 0.000000 0.000000 1.200000 3.500000 4.000000 -0.362143 -1.285274 -0.939591 0.204641 -0.106438 1.200000 3.500000 4.000000
O O pps 9.460772 -1.211748 -0.581016 0.000000 0.000000 1.200000 3.500000 4.000000 -0.312044 0.121814 -2.519352 1.681266 -0.644566 1.200000 3.500000 4.000000
O O ppp -4.494595 -2.709223 -0.284124 0.000000 0.000000 1.200000 3.500000 4.000000 0.193010 -2.168462 -0.580629 -0.105104 0.004891 1.200000 3.500000 4.000000
H O sss -12.230931 -1.808632 -0.421164 0.000000 0.000000 1.000000 3.500000 4.000000 0.404725 -1.702546 -0.707938 0.074904 -0.039922 1.000000 3.500000 4.000000
H O sps 9.466088 -1.321262 -0.386336 0.000000 0.000000 1.000000 3.500000 4.000000 -0.447660 -0.952979 -1.163537 0.400616 -0.156965 1.000000 3.500000 4.000000
N N sss -7.710330 -2.365312 -0.525527 0.000000 0.000000 1.500000 3.500000 4.000000 0.231654 -1.879002 -0.572765 -0.004579 -0.031106 1.500000 3.500000 4.000000
N N sps 8.222314 -1.612118 -0.690081 0.000000 0.000000 1.500000 3.500000 4.000000 -0.305271 -1.385158 -0.751032 0.114531 -0.090839 1.500000 3.500000 4.000000
N N pps 7.178570 -1.176467 -0.571049 0.000000 0.000000 1.500000 3.500000 4.000000 -0.324668 -0.547805 -1.638658 1.495168 -0.827868 1.500000 3.500000 4.000000
N N ppp -2.829344 -2.408049 -0.387709 0.000000 0.000000 1.500000 3.500000 4.000000 0.142909 -2.162036 -0.571942 -0.071640 -0.004682 1.500000 3.500000 4.000000
H N sss -12.095890 -1.519057 -0.277247 0.000000 0.000000 1.000000 3.500000 4.000000 0.446693 -1.500463 -0.657448 0.065741 -0.037004 1.000000 3.500000 4.000000
H N sps 9.851338 -1.231616 -0.370836 0.000000 0.000000 1.000000 3.500000 4.000000 -0.501530 -0.785734 -1.123232 0.394878 -0.148501 1.000000 3.500000 4.000000

7
examples/QUANTUM/LATTE/TBparam_generic/electrons.dat Normal file
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@ -0,0 +1,7 @@
Noelem= 5
Element basis Numel Es Ep Ed Ef Mass HubbardU Wss Wpp Wdd Wff
N sp 5.0 -18.58 -7.09 0.0 0.0 14.0067 15.93 0.0 -0.6950 0.0 0.0
O sp 6.0 -23.96 -9.02 0.0 0.0 15.9994 12.15 0.0 -0.7577 0.0 0.0
H s 1.0 -6.35 0.0 0.0 0.0 1.0079 12.85 -1.7937 0.0 0.0 0.0
C sp 4.0 -13.75 -5.28 0.0 0.0 12.01 10.0 0.0 -0.621 0.0 0.0
Ti sd 4.0 -5.5 0.0 -3.0 0.0 47.867 10.0 0.0 0.0 0.0 0.0

12
examples/QUANTUM/LATTE/TBparam_generic/ppots.nonortho Normal file
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@ -0,0 +1,12 @@
Nopps= 10
Ele1 Ele2 A0 A1 A2 A3 A4 A5 A6 C R1 Rcut
N O 13.182426 20.050322 -46.806321 38.206953 -12.319656 0.000000 0.000000 0.000000 1.600000 1.700000
C N 88.953762 10.294988 -27.706877 22.101434 -6.836438 0.000000 0.000000 0.000000 1.600000 1.700000
C O 0.944093 30.116337 -59.608215 45.107654 -13.178839 0.000000 0.000000 0.000000 1.600000 1.700000
C H 104.889589 3.971095 -23.823043 26.408093 -11.317522 0.000000 0.000000 0.000000 1.200000 1.300000
C C 3.962931 24.467772 -51.156024 39.031644 -11.342979 0.000000 0.000000 0.000000 1.600000 1.700000
H H 38.512100 3.887860 -37.769100 57.083500 -34.512200 0.000000 0.000000 0.000000 0.900000 1.000000
N N 43.228899 15.004605 -36.621777 29.234888 -8.912743 0.000000 0.000000 0.000000 1.600000 1.700000
N H 0.625470 28.081241 -63.414297 53.286361 -17.352234 0.000000 0.000000 0.000000 1.300000 1.400000
O O 10.999870 19.303033 -45.747853 37.946431 -11.935755 0.000000 0.000000 0.000000 1.500000 1.600000
O H 0.481176 33.175383 -81.158683 74.935408 -26.792315 0.000000 0.000000 0.000000 1.200000 1.300000

23
examples/QUANTUM/LATTE/data.ch4 Normal file
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@ -0,0 +1,23 @@
LAMMPS Description
5 atoms
2 atom types
0.0000000000000000 19.523000000000000 xlo xhi
0.0000000000000000 12.757999999999999 ylo yhi
0.0000000000000000 11.692000000000000 zlo zhi
0.0000000000000000 0.0000000000000000 0.0000000000000000 xy xz yz
Masses
1 12.010000000000000
2 1.0078250169754028
Atoms
1 1 1 0.0 -9.16600 2.05200 0.00000
2 1 2 0.0 -8.09600 2.05200 0.00000
3 1 2 0.0 -9.52300 2.75800 -0.72000
4 1 2 0.0 -9.52300 2.32200 0.97200
5 1 2 0.0 -9.52300 1.07500 -0.25200

49
examples/QUANTUM/LATTE/data.graphene Normal file
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@ -0,0 +1,49 @@
LAMMPS Description
32 atoms
1 atom types
0.0000000000000000 10.000000000000000 xlo xhi
0.0000000000000000 8.0000000000000000 ylo yhi
0.0000000000000000 20.000000000000000 zlo zhi
4.8985871965894128E-016 1.2246467991473533E-015 1.2246467991473533E-015 xy xz yz
Masses
1 12.010000000000000
Atoms
1 1 1 0.0 4.93100 4.25000 0.00500
2 1 1 0.0 8.62100 2.12100 0.14000
3 1 1 0.0 3.70700 2.12600 0.14700
4 1 1 0.0 7.38200 4.25400 0.07800
5 1 1 0.0 2.47900 4.25400 0.08000
6 1 1 0.0 6.15800 6.37400 -0.01000
7 1 1 0.0 1.23700 6.38300 0.06600
8 1 1 0.0 1.24000 2.12100 0.14600
9 1 1 0.0 6.15500 2.12600 0.12900
10 1 1 0.0 0.00700 4.25200 0.12200
11 1 1 0.0 8.62100 6.38500 0.04100
12 1 1 0.0 3.70000 6.37400 -0.01000
13 1 1 0.0 0.00600 1.41600 0.13000
14 1 1 0.0 4.93000 1.40800 0.14700
15 1 1 0.0 8.61800 3.54600 0.11500
16 1 1 0.0 3.70800 3.55300 0.08400
17 1 1 0.0 7.39400 5.68000 0.03500
18 1 1 0.0 2.46500 5.68000 0.03500
19 1 1 0.0 6.16000 7.80500 0.02700
20 1 1 0.0 1.23800 7.81100 0.06000
21 1 1 0.0 2.47300 1.41800 0.16100
22 1 1 0.0 7.38900 1.41700 0.14800
23 1 1 0.0 1.24200 3.54700 0.12600
24 1 1 0.0 6.15300 3.55300 0.07400
25 1 1 0.0 0.00700 5.67800 0.09700
26 1 1 0.0 4.93100 5.66800 -0.03100
27 1 1 0.0 8.62000 7.81300 0.03900
28 1 1 0.0 3.70100 7.80200 0.03700
29 1 1 0.0 0.00700 -0.01000 0.08900
30 1 1 0.0 4.93100 -0.01500 0.16100
31 1 1 0.0 2.47300 -0.01200 0.14400
32 1 1 0.0 7.38900 -0.01300 0.14800

63
examples/QUANTUM/LATTE/data.sucrose Normal file
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@ -0,0 +1,63 @@
LAMMPS Description
45 atoms
3 atom types
0.0000000000000000 17.202999999999999 xlo xhi
0.0000000000000000 18.009000000000000 ylo yhi
0.0000000000000000 21.643000000000001 zlo zhi
Masses
1 15.9994
2 12.01
3 1.0079
Atoms
1 1 1 0.0 8.62700 8.66700 12.48600
2 1 1 0.0 9.11200 9.11800 10.27300
3 1 1 0.0 8.45700 11.33100 10.49000
4 1 1 0.0 11.72600 8.36500 10.66700
5 1 1 0.0 8.06500 8.99400 7.93600
6 1 2 0.0 9.62800 9.07200 11.59100
7 1 3 0.0 9.90900 10.08300 11.89200
8 1 2 0.0 9.07000 10.40400 9.64000
9 1 1 0.0 6.14600 11.61000 8.00500
10 1 1 0.0 11.07200 10.13000 8.37600
11 1 1 0.0 6.10200 10.00900 11.62100
12 1 2 0.0 8.14000 10.29100 8.45100
13 1 3 0.0 8.49000 10.91200 7.62300
14 1 1 0.0 7.41500 7.08400 14.43400
15 1 2 0.0 10.75100 8.07000 11.65100
16 1 3 0.0 11.24000 8.11800 12.63400
17 1 2 0.0 7.09000 11.63400 10.17000
18 1 3 0.0 7.06900 12.69800 9.91100
19 1 2 0.0 7.97200 7.44200 12.14000
20 1 3 0.0 7.54700 7.58300 11.13800
21 1 1 0.0 11.24900 5.73000 11.78600
22 1 2 0.0 10.26800 6.65900 11.37300
23 1 3 0.0 10.12300 6.53400 10.29200
24 1 2 0.0 6.78400 10.79500 8.95500
25 1 3 0.0 6.12100 9.95500 9.19600
26 1 2 0.0 10.47500 10.88300 9.39800
27 1 3 0.0 10.49500 11.92100 9.06900
28 1 3 0.0 11.09100 10.82000 10.30900
29 1 2 0.0 8.99100 6.32000 12.11700
30 1 3 0.0 9.23100 6.01100 13.14400
31 1 2 0.0 6.86600 7.25300 13.14500
32 1 3 0.0 6.17700 8.10100 13.15700
33 1 3 0.0 6.28900 6.35300 12.94300
34 1 2 0.0 6.24000 11.39400 11.39300
35 1 3 0.0 6.66500 11.86500 12.28300
36 1 3 0.0 5.23100 11.78100 11.26000
37 1 1 0.0 8.34300 5.24100 11.48000
38 1 3 0.0 12.00100 9.28600 10.78200
39 1 3 0.0 12.06300 5.97500 11.33000
40 1 3 0.0 6.99600 9.67600 11.79700
41 1 3 0.0 7.93700 7.87600 14.60900
42 1 3 0.0 10.95500 9.19800 8.60700
43 1 3 0.0 5.94400 11.05900 7.24100
44 1 3 0.0 7.94900 8.39500 8.68400
45 1 3 0.0 8.96400 4.50300 11.48800

39
examples/QUANTUM/LATTE/in.ch4 Normal file
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# simple CH4 model with LATTE
units metal
atom_style full
read_data data.ch4
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements C H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 100

41
examples/QUANTUM/LATTE/in.ch4.plugin Normal file
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@ -0,0 +1,41 @@
# simple CH4 model with LATTE
units metal
atom_style full
read_data data.ch4
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements C H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
extra latte.in.generic command "run 100"

39
examples/QUANTUM/LATTE/in.graphene Normal file
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@ -0,0 +1,39 @@
# graphene model with LATTE
units metal
atom_style full
read_data data.graphene
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 100.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements C
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 5
run 20

41
examples/QUANTUM/LATTE/in.graphene.plugin Normal file
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@ -0,0 +1,41 @@
# graphene model with LATTE
units metal
atom_style full
read_data data.graphene
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 100.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements C
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 5
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
extra latte.in.generic command "run 20"

1
examples/QUANTUM/LATTE/in.series
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@ -9,7 +9,6 @@ label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data data.${files}

1
examples/QUANTUM/LATTE/in.series.plugin
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@ -7,7 +7,6 @@ label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data data.${files}

39
examples/QUANTUM/LATTE/in.sucrose Normal file
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@ -0,0 +1,39 @@
# sucrose model with LATTE
units metal
atom_style full
read_data data.sucrose
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 100.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements O C H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 100

41
examples/QUANTUM/LATTE/in.sucrose.plugin Normal file
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@ -0,0 +1,41 @@
# sucrose model with LATTE
units metal
atom_style full
read_data data.sucrose
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 100.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements O C H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
extra latte.in.generic command "run 100"

3
examples/QUANTUM/LATTE/in.uo2
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@ -2,7 +2,6 @@
units metal
atom_style full
atom_modify sort 0 0.0
read_data data.2uo2
@ -18,7 +17,7 @@ fix 1 all nve
fix 2 all mdi/qm virial yes elements U O
thermo_style custom step temp pe etotal press
thermo 1
thermo 5
#dump 1 all custom 1 dump.aimd.mpi &
# id type x y z vx vy vz fx fy fz

7
examples/QUANTUM/LATTE/in.uo2.plugin
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@ -1,8 +1,7 @@
# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data data.2uo2
@ -18,9 +17,9 @@ fix 1 all nve
fix 2 all mdi/qm virial yes elements U O
thermo_style custom step temp pe etotal press
thermo 1
thermo 5
#dump 1 all custom 1 dump.aimd.plugin &
#dump 1 all custom 1 dump.aimd.mpi &
# id type x y z vx vy vz fx fy fz
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &

2
examples/QUANTUM/LATTE/in.water
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@ -2,7 +2,6 @@
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water
@ -30,7 +29,6 @@ timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements O H
#fix 2 all latte
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press

39
examples/QUANTUM/LATTE/in.water.min Normal file
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@ -0,0 +1,39 @@
# minimize water model with LATTE and FIRE
units metal
atom_style full
read_data data.water
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
fix 1 all nve
fix 2 all mdi/qm virial yes elements O H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# minimization
thermo 10
min_style fire
minimize 1.0e-4 1.0e-4 500 500

41
examples/QUANTUM/LATTE/in.water.min.plugin Normal file
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@ -0,0 +1,41 @@
# minimize water model with LATTE and FIRE
units metal
atom_style full
read_data data.water
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
fix 1 all nve
fix 2 all mdi/qm virial yes elements O H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# minimization
thermo 10
min_style fire
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
extra latte.in.water command "minimize 1.0e-4 1.0e-4 500 500"

1
examples/QUANTUM/LATTE/in.water.plugin
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@ -2,7 +2,6 @@
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water

32
examples/QUANTUM/LATTE/latte.in.generic Normal file
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@ -0,0 +1,32 @@
LATTE INPUT FILE
================
#This input file resumes the content of MDcontroller and TBparam/control.in
#The parser will only read it is present inside the running folder.
#In case this file is not present Latte will read the two files as original.
#The order of the keywords is not important in this file.
#To get a full description of these keywords please see:
## https://github.com/lanl/LATTE/blob/master/Manual/LATTE_manual.pdf
#General controls
CONTROL{
XCONTROL= 1
BASISTYPE= NONORTHO
PARAMPATH= "./TBparam_generic"
KBT= 0.0
ENTROPYKIND= 1
PPOTON= 1
SPINON= 0 SPINTOL= 1.0e-4
ELECTRO= 1 ELECMETH= 0 ELEC_QTOL= 1.0e-8
MAXSCF= 450
BREAKTOL= 1.0E-6 MINSP2ITER= 22 SP2CONV= REL
FULLQCONV= 1 QITER= 3
QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25
SPARSEON= 0 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4
MSPARSE= 1500
SKIN= 1.0
CHARGE= 0
XBO= 1
XBODISON= 1
XBODISORDER= 5
KON= 0
}

2
examples/QUANTUM/LATTE/latte.in.uo2
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@ -12,7 +12,7 @@ CONTROL{
ENTROPYKIND= 1
PPOTON= 2 VDWON= 0
SPINON= 0 SPINTOL= 1.0e-4
ELECTRO= 1 ELECMETH= 0 ELEC_ETOL= 0.001 ELEC_QTOL= 1.0e-12
ELECTRO= 1 ELECMETH= 0 ELEC_ETOL= 0.001 ELEC_QTOL= 1.0e-5
COULACC= 1.0e-6 COULCUT= -500.0 COULR1= 500.0
MAXSCF= 250
BREAKTOL= 1.0E-12 MINSP2ITER= 22 SP2CONV= REL

109
examples/QUANTUM/LATTE/log.8Feb23.ch4.mpi.1 Normal file
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LAMMPS (22 Dec 2022)
# simple CH4 model with LATTE
units metal
atom_style full
read_data data.ch4
Reading data file ...
triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
5 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements C H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 100
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 20 13 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.027 | 6.027 | 6.027 Mbytes
Step Temp PotEng TotEng Press
0 0 -23.980353 -23.980353 348.02718
10 19.123151 -23.990297 -23.98041 18.774333
20 0.32743246 -23.980525 -23.980355 -336.7411
30 18.229142 -23.989832 -23.980407 -72.30124
40 1.3944306 -23.981078 -23.980357 335.25084
50 17.34967 -23.989376 -23.980405 109.38135
60 2.7948439 -23.981807 -23.980362 -313.70127
70 14.957352 -23.98813 -23.980397 -157.44458
80 5.1636049 -23.983039 -23.980369 297.94883
90 13.368191 -23.987306 -23.980394 192.91153
100 7.0848846 -23.984037 -23.980374 -269.0214
Loop time of 0.206985 on 1 procs for 100 steps with 5 atoms
Performance: 10.436 ns/day, 2.300 hours/ns, 483.127 timesteps/s, 2.416 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.489e-06 | 3.489e-06 | 3.489e-06 | 0.0 | 0.00
Bond | 2.248e-06 | 2.248e-06 | 2.248e-06 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.0075e-05 | 1.0075e-05 | 1.0075e-05 | 0.0 | 0.00
Output | 3.7574e-05 | 3.7574e-05 | 3.7574e-05 | 0.0 | 0.02
Modify | 0.20692 | 0.20692 | 0.20692 | 0.0 | 99.97
Other | | 1.617e-05 | | | 0.01
Nlocal: 5 ave 5 max 5 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: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 10
Ave neighs/atom = 2
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

111
examples/QUANTUM/LATTE/log.8Feb23.ch4.plugin.1 Normal file
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@ -0,0 +1,111 @@
LAMMPS (22 Dec 2022)
# simple CH4 model with LATTE
units metal
atom_style full
read_data data.ch4
Reading data file ...
triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
5 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements C H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.generic command "run 100"
run 100
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 20 13 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.027 | 6.027 | 6.027 Mbytes
Step Temp PotEng TotEng Press
0 0 -23.980353 -23.980353 348.02718
10 19.123151 -23.990297 -23.98041 18.774333
20 0.32743246 -23.980525 -23.980355 -336.7411
30 18.229142 -23.989832 -23.980407 -72.30124
40 1.3944306 -23.981078 -23.980357 335.25084
50 17.34967 -23.989376 -23.980405 109.38135
60 2.7948439 -23.981807 -23.980362 -313.70127
70 14.957352 -23.98813 -23.980397 -157.44458
80 5.1636049 -23.983039 -23.980369 297.94883
90 13.368191 -23.987306 -23.980394 192.91153
100 7.0848846 -23.984037 -23.980374 -269.0214
Loop time of 0.136887 on 1 procs for 100 steps with 5 atoms
Performance: 15.779 ns/day, 1.521 hours/ns, 730.528 timesteps/s, 3.653 katom-step/s
161.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.73e-06 | 9.73e-06 | 9.73e-06 | 0.0 | 0.01
Bond | 3.788e-06 | 3.788e-06 | 3.788e-06 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.8569e-05 | 2.8569e-05 | 2.8569e-05 | 0.0 | 0.02
Output | 9.5789e-05 | 9.5789e-05 | 9.5789e-05 | 0.0 | 0.07
Modify | 0.1367 | 0.1367 | 0.1367 | 0.0 | 99.86
Other | | 4.791e-05 | | | 0.03
Nlocal: 5 ave 5 max 5 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: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 10
Ave neighs/atom = 2
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

103
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LAMMPS (22 Dec 2022)
# graphene model with LATTE
units metal
atom_style full
read_data data.graphene
Reading data file ...
triclinic box = (0 0 0) to (10 8 20) with tilt (4.8985872e-16 1.2246468e-15 1.2246468e-15)
1 by 1 by 1 MPI processor grid
reading atoms ...
32 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 100.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements C
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 5
run 20
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 11 9 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.03 | 6.03 | 6.03 Mbytes
Step Temp PotEng TotEng Press
0 100 -247.46002 -247.05931 63327.854
5 826.57726 -250.37499 -247.06284 62186.684
10 2683.9104 -257.82775 -247.07314 59699.92
15 4697.8879 -265.91019 -247.08545 57703.843
20 5758.1468 -270.16276 -247.0895 57792.304
Loop time of 3.05205 on 1 procs for 20 steps with 32 atoms
Performance: 0.142 ns/day, 169.558 hours/ns, 6.553 timesteps/s, 209.695 atom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.69e-06 | 5.69e-06 | 5.69e-06 | 0.0 | 0.00
Bond | 9.35e-07 | 9.35e-07 | 9.35e-07 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3983e-05 | 1.3983e-05 | 1.3983e-05 | 0.0 | 0.00
Output | 3.6243e-05 | 3.6243e-05 | 3.6243e-05 | 0.0 | 0.00
Modify | 3.052 | 3.052 | 3.052 | 0.0 |100.00
Other | | 1.742e-05 | | | 0.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 48 ave 48 max 48 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 48
Ave neighs/atom = 1.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

105
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LAMMPS (22 Dec 2022)
# graphene model with LATTE
units metal
atom_style full
read_data data.graphene
Reading data file ...
triclinic box = (0 0 0) to (10 8 20) with tilt (4.8985872e-16 1.2246468e-15 1.2246468e-15)
1 by 1 by 1 MPI processor grid
reading atoms ...
32 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 100.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements C
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 5
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.generic command "run 20"
run 20
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 11 9 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.03 | 6.03 | 6.03 Mbytes
Step Temp PotEng TotEng Press
0 100 -247.46002 -247.05931 63327.854
5 826.57726 -250.37499 -247.06284 62186.684
10 2683.9104 -257.82775 -247.07314 59699.92
15 4697.8879 -265.91019 -247.08545 57703.843
20 5758.1468 -270.16276 -247.0895 57792.304
Loop time of 4.91692 on 1 procs for 20 steps with 32 atoms
Performance: 0.088 ns/day, 273.162 hours/ns, 4.068 timesteps/s, 130.163 atom-step/s
564.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2813e-05 | 1.2813e-05 | 1.2813e-05 | 0.0 | 0.00
Bond | 2.863e-06 | 2.863e-06 | 2.863e-06 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 4.143e-05 | 4.143e-05 | 4.143e-05 | 0.0 | 0.00
Output | 0.047766 | 0.047766 | 0.047766 | 0.0 | 0.97
Modify | 4.869 | 4.869 | 4.869 | 0.0 | 99.03
Other | | 6.209e-05 | | | 0.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 48 ave 48 max 48 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 48
Ave neighs/atom = 1.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05

231
examples/QUANTUM/LATTE/log.8Feb23.series.mpi.1 Normal file
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LAMMPS (22 Dec 2022)
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI stand-alone mode
variable files index 2uo2 3uo2 4uo2
mdi connect
label LOOP
units metal
atom_style full
read_data data.${files}
read_data data.2uo2
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements U O connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -50.539026 -50.539026 -120855.18
Loop time of 2.54e-07 on 1 procs for 0 steps with 6 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.54e-07 | | |100.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
#write_dump all custom dump.series.mpi.${files} # id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP
units metal
atom_style full
read_data data.${files}
read_data data.3uo2
Reading data file ...
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
9 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements U O connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -78.155585 -78.155585 -99929.253
Loop time of 3.78e-07 on 1 procs for 0 steps with 9 atoms
264.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.78e-07 | | |100.00
Nlocal: 9 ave 9 max 9 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
#write_dump all custom dump.series.mpi.${files} # id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP
units metal
atom_style full
read_data data.${files}
read_data data.4uo2
Reading data file ...
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
12 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements U O connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -102.35715 -102.35715 -31036.694
Loop time of 4.53e-07 on 1 procs for 0 steps with 12 atoms
220.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.53e-07 | | |100.00
Nlocal: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5 ave 5 max 5 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
#write_dump all custom dump.series.mpi.${files} # id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP
mdi exit
Total wall time: 0:00:00

227
examples/QUANTUM/LATTE/log.8Feb23.series.plugin.1 Normal file
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LAMMPS (22 Dec 2022)
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI plugin mode
variable files index 2uo2 3uo2 4uo2
label LOOP
units metal
atom_style full
read_data data.${files}
read_data data.2uo2
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements U O
fix_modify 1 energy yes
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.uo2 command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -50.539026 -50.539026 -120855.18
Loop time of 7.62e-07 on 1 procs for 0 steps with 6 atoms
524.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 7.62e-07 | | |100.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
#write_dump all custom dump.series.plugin.${files} # id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP
units metal
atom_style full
read_data data.${files}
read_data data.3uo2
Reading data file ...
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
9 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements U O
fix_modify 1 energy yes
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.uo2 command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -78.155585 -78.155585 -99929.253
Loop time of 6.86e-07 on 1 procs for 0 steps with 9 atoms
583.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 6.86e-07 | | |100.00
Nlocal: 9 ave 9 max 9 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
#write_dump all custom dump.series.plugin.${files} # id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP
units metal
atom_style full
read_data data.${files}
read_data data.4uo2
Reading data file ...
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
12 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements U O
fix_modify 1 energy yes
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.uo2 command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -102.35715 -102.35715 -31036.694
Loop time of 9.07e-07 on 1 procs for 0 steps with 12 atoms
882.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.07e-07 | | |100.00
Nlocal: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5 ave 5 max 5 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
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
#write_dump all custom dump.series.plugin.${files} # id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP
Total wall time: 0:00:00

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LAMMPS (22 Dec 2022)
# sucrose model with LATTE
units metal
atom_style full
read_data data.sucrose
Reading data file ...
orthogonal box = (0 0 0) to (17.203 18.009 21.643)
1 by 1 by 1 MPI processor grid
reading atoms ...
45 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 100.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements O C H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 100
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 18 19 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.055 | 6.055 | 6.055 Mbytes
Step Temp PotEng TotEng Press
0 100 -251.26616 -250.69742 107.21668
10 66.857941 -251.07691 -250.69666 -492.79612
20 59.63791 -251.03635 -250.69717 -248.43262
30 37.423913 -250.90951 -250.69666 188.29378
40 58.409162 -251.0293 -250.6971 -237.97667
50 59.243304 -251.0339 -250.69695 -638.8034
60 52.981345 -250.99824 -250.69691 -316.59797
70 43.705344 -250.9456 -250.69703 85.920691
80 38.818553 -250.91757 -250.69679 -13.26722
90 53.942805 -251.00391 -250.69711 -245.17309
100 49.969604 -250.98104 -250.69684 -243.79969
Loop time of 16.5307 on 1 procs for 100 steps with 45 atoms
Performance: 0.131 ns/day, 183.675 hours/ns, 6.049 timesteps/s, 272.220 atom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8626e-05 | 1.8626e-05 | 1.8626e-05 | 0.0 | 0.00
Bond | 5.206e-06 | 5.206e-06 | 5.206e-06 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3114e-05 | 1.3114e-05 | 1.3114e-05 | 0.0 | 0.00
Output | 0.00013326 | 0.00013326 | 0.00013326 | 0.0 | 0.00
Modify | 16.531 | 16.531 | 16.531 | 0.0 |100.00
Other | | 6.971e-05 | | | 0.00
Nlocal: 45 ave 45 max 45 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: 59 ave 59 max 59 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 59
Ave neighs/atom = 1.3111111
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:16

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LAMMPS (22 Dec 2022)
# sucrose model with LATTE
units metal
atom_style full
read_data data.sucrose
Reading data file ...
orthogonal box = (0 0 0) to (17.203 18.009 21.643)
1 by 1 by 1 MPI processor grid
reading atoms ...
45 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 100.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements O C H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.generic command "run 100"
run 100
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 18 19 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.055 | 6.055 | 6.055 Mbytes
Step Temp PotEng TotEng Press
0 100 -251.26616 -250.69742 107.21668
10 66.857941 -251.07691 -250.69666 -492.79612
20 59.63791 -251.03635 -250.69717 -248.43262
30 37.423913 -250.90951 -250.69666 188.29378
40 58.409162 -251.0293 -250.6971 -237.97667
50 59.243304 -251.0339 -250.69695 -638.8034
60 52.981345 -250.99824 -250.69691 -316.59797
70 43.705344 -250.9456 -250.69703 85.920691
80 38.818553 -250.91757 -250.69679 -13.26722
90 53.942805 -251.00391 -250.69711 -245.17309
100 49.969604 -250.98104 -250.69684 -243.79969
Loop time of 26.8476 on 1 procs for 100 steps with 45 atoms
Performance: 0.080 ns/day, 298.306 hours/ns, 3.725 timesteps/s, 167.613 atom-step/s
553.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.7375e-05 | 6.7375e-05 | 6.7375e-05 | 0.0 | 0.00
Bond | 1.8658e-05 | 1.8658e-05 | 1.8658e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.5578e-05 | 8.5578e-05 | 8.5578e-05 | 0.0 | 0.00
Output | 0.099643 | 0.099643 | 0.099643 | 0.0 | 0.37
Modify | 26.747 | 26.747 | 26.747 | 0.0 | 99.63
Other | | 0.0003245 | | | 0.00
Nlocal: 45 ave 45 max 45 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: 59 ave 59 max 59 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 59
Ave neighs/atom = 1.3111111
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:27

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LAMMPS (22 Dec 2022)
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
units metal
atom_style full
read_data data.2uo2
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements U O
thermo_style custom step temp pe etotal press
thermo 5
#dump 1 all custom 1 dump.aimd.mpi # id type x y z vx vy vz fx fy fz
run 20
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 300 -50.539026 -50.345136 -120197.58
5 349.9977 -50.576715 -50.350511 -119686.74
10 428.81071 -50.636477 -50.359336 -118824.24
15 532.96198 -50.716083 -50.371629 -117598.48
20 657.59195 -50.812448 -50.387446 -115993.96
Loop time of 0.685388 on 1 procs for 20 steps with 6 atoms
Performance: 0.630 ns/day, 38.077 hours/ns, 29.181 timesteps/s, 175.083 atom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 5.62e-07 | 5.62e-07 | 5.62e-07 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 3.734e-06 | 3.734e-06 | 3.734e-06 | 0.0 | 0.00
Output | 2.4426e-05 | 2.4426e-05 | 2.4426e-05 | 0.0 | 0.00
Modify | 0.68535 | 0.68535 | 0.68535 | 0.0 |100.00
Other | | 5.523e-06 | | | 0.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 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
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (22 Dec 2022)
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
units metal
atom_style full
read_data data.2uo2
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements U O
thermo_style custom step temp pe etotal press
thermo 5
#dump 1 all custom 1 dump.aimd.mpi # id type x y z vx vy vz fx fy fz
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.uo2 command "run 20"
run 20
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2344)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 300 -50.539026 -50.345136 -120197.58
5 349.9977 -50.576715 -50.350511 -119686.74
10 428.81071 -50.636477 -50.359336 -118824.24
15 532.96198 -50.716083 -50.371629 -117598.48
20 657.59195 -50.812448 -50.387446 -115993.96
Loop time of 0.493269 on 1 procs for 20 steps with 6 atoms
Performance: 0.876 ns/day, 27.404 hours/ns, 40.546 timesteps/s, 243.275 atom-step/s
326.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 2.061e-06 | 2.061e-06 | 2.061e-06 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.411e-05 | 1.411e-05 | 1.411e-05 | 0.0 | 0.00
Output | 5.6957e-05 | 5.6957e-05 | 5.6957e-05 | 0.0 | 0.01
Modify | 0.49316 | 0.49316 | 0.49316 | 0.0 | 99.98
Other | | 3.15e-05 | | | 0.01
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 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
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (22 Dec 2022)
# minimize water model with LATTE and FIRE
units metal
atom_style full
read_data data.water
Reading data file ...
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
1 by 1 by 1 MPI processor grid
reading atoms ...
24 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
fix 1 all nve
fix 2 all mdi/qm virial yes elements O H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# minimization
thermo 10
min_style fire
minimize 1.0e-4 1.0e-4 500 500
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback abcfire
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes no
Per MPI rank memory allocation (min/avg/max) = 6.005 | 6.005 | 6.005 Mbytes
Step Temp PotEng TotEng Press
0 0 0 0 0
10 899.1524 -108.14682 -105.47365 73033.936
20 1939.7634 -109.75294 -103.98606 40647.182
30 4.831893 -110.23114 -110.21677 5660.776
40 50.735819 -110.29132 -110.14048 4890.8986
50 153.92 -110.3956 -109.938 5046.3911
60 3.0178397 -110.52031 -110.51134 1964.2114
70 26.161763 -110.55445 -110.47667 1839.5114
78 69.53487 -110.60152 -110.39479 2086.0227
Loop time of 3.38506 on 1 procs for 78 steps with 24 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
0 -110.594257523513 -110.601518955915
Force two-norm initial, final = 0 0.28249145
Force max component initial, final = 0 0.096323097
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 78 81
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.116e-06 | 7.116e-06 | 7.116e-06 | 0.0 | 0.00
Bond | 2.222e-06 | 2.222e-06 | 2.222e-06 | 0.0 | 0.00
Neigh | 1.7255e-05 | 1.7255e-05 | 1.7255e-05 | 0.0 | 0.00
Comm | 4.8011e-05 | 4.8011e-05 | 4.8011e-05 | 0.0 | 0.00
Output | 4.5107e-05 | 4.5107e-05 | 4.5107e-05 | 0.0 | 0.00
Modify | 3.3849 | 3.3849 | 3.3849 | 0.0 | 99.99
Other | | 6.706e-05 | | | 0.00
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 75 ave 75 max 75 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 26 ave 26 max 26 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 26
Ave neighs/atom = 1.0833333
Ave special neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (22 Dec 2022)
# minimize water model with LATTE and FIRE
units metal
atom_style full
read_data data.water
Reading data file ...
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
1 by 1 by 1 MPI processor grid
reading atoms ...
24 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
fix 1 all nve
fix 2 all mdi/qm virial yes elements O H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# minimization
thermo 10
min_style fire
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.water command "minimize 1.0e-4 1.0e-4 500 500"
minimize 1.0e-4 1.0e-4 500 500
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback abcfire
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes no
Per MPI rank memory allocation (min/avg/max) = 6.005 | 6.005 | 6.005 Mbytes
Step Temp PotEng TotEng Press
0 0 0 0 0
10 899.1524 -108.14682 -105.47365 73033.936
20 1939.7634 -109.75294 -103.98606 40647.182
30 4.831893 -110.23114 -110.21677 5660.776
40 50.735819 -110.29132 -110.14048 4890.8986
50 153.92 -110.3956 -109.938 5046.3911
60 3.0178397 -110.52031 -110.51134 1964.2114
70 26.161763 -110.55445 -110.47667 1839.5114
78 69.53487 -110.60152 -110.39479 2086.0227
Loop time of 2.7873 on 1 procs for 78 steps with 24 atoms
381.8% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
0 -110.594257523513 -110.601518955916
Force two-norm initial, final = 0 0.28249145
Force max component initial, final = 0 0.096323097
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 78 81
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5459e-05 | 2.5459e-05 | 2.5459e-05 | 0.0 | 0.00
Bond | 6.18e-06 | 6.18e-06 | 6.18e-06 | 0.0 | 0.00
Neigh | 2.0887e-05 | 2.0887e-05 | 2.0887e-05 | 0.0 | 0.00
Comm | 8.5176e-05 | 8.5176e-05 | 8.5176e-05 | 0.0 | 0.00
Output | 9.412e-05 | 9.412e-05 | 9.412e-05 | 0.0 | 0.00
Modify | 2.7869 | 2.7869 | 2.7869 | 0.0 | 99.98
Other | | 0.0002202 | | | 0.01
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 75 ave 75 max 75 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 26 ave 26 max 26 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 26
Ave neighs/atom = 1.0833333
Ave special neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (22 Dec 2022)
# simple water model with LATTE
units metal
atom_style full
read_data data.water
Reading data file ...
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
1 by 1 by 1 MPI processor grid
reading atoms ...
24 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements O H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 100
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.005 | 6.005 | 6.005 Mbytes
Step Temp PotEng TotEng Press
0 0 -104.95596 -104.95596 48235.444
10 336.53106 -105.96027 -104.95977 97996.851
20 529.06409 -106.53023 -104.95733 131519.85
30 753.62603 -107.19952 -104.959 49296.662
40 716.65647 -107.08803 -104.95742 28307.122
50 824.04393 -107.40823 -104.95836 102167.59
60 933.56146 -107.73479 -104.95933 92508.518
70 851.18489 -107.48767 -104.95711 13993.264
80 999.80278 -107.93147 -104.95907 36700.735
90 998.77487 -107.9257 -104.95636 107233.54
100 1281.4438 -108.76963 -104.95992 49702.389
Loop time of 3.33625 on 1 procs for 100 steps with 24 atoms
Performance: 0.647 ns/day, 37.069 hours/ns, 29.974 timesteps/s, 719.370 atom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.741e-06 | 6.741e-06 | 6.741e-06 | 0.0 | 0.00
Bond | 2.864e-06 | 2.864e-06 | 2.864e-06 | 0.0 | 0.00
Neigh | 1.816e-05 | 1.816e-05 | 1.816e-05 | 0.0 | 0.00
Comm | 7.144e-05 | 7.144e-05 | 7.144e-05 | 0.0 | 0.00
Output | 5.3539e-05 | 5.3539e-05 | 5.3539e-05 | 0.0 | 0.00
Modify | 3.3361 | 3.3361 | 3.3361 | 0.0 | 99.99
Other | | 2.634e-05 | | | 0.00
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 77 ave 77 max 77 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 31 ave 31 max 31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31
Ave neighs/atom = 1.2916667
Ave special neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:03

111
examples/QUANTUM/LATTE/log.8Feb23.water.plugin.1 Normal file
View File

@ -0,0 +1,111 @@
LAMMPS (22 Dec 2022)
# simple water model with LATTE
units metal
atom_style full
read_data data.water
Reading data file ...
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
1 by 1 by 1 MPI processor grid
reading atoms ...
24 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements O H
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.water command "run 100"
run 100
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.005 | 6.005 | 6.005 Mbytes
Step Temp PotEng TotEng Press
0 0 -104.95596 -104.95596 48235.444
10 336.53106 -105.96027 -104.95977 97996.851
20 529.06409 -106.53023 -104.95733 131519.85
30 753.62603 -107.19952 -104.959 49296.662
40 716.65647 -107.08803 -104.95742 28307.122
50 824.04393 -107.40823 -104.95836 102167.59
60 933.56146 -107.73479 -104.95933 92508.518
70 851.18489 -107.48767 -104.95711 13993.264
80 999.80278 -107.93147 -104.95907 36700.735
90 998.77487 -107.9257 -104.95636 107233.54
100 1281.4438 -108.76963 -104.95992 49702.389
Loop time of 3.97845 on 1 procs for 100 steps with 24 atoms
Performance: 0.543 ns/day, 44.205 hours/ns, 25.135 timesteps/s, 603.251 atom-step/s
369.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8286e-05 | 2.8286e-05 | 2.8286e-05 | 0.0 | 0.00
Bond | 7.551e-06 | 7.551e-06 | 7.551e-06 | 0.0 | 0.00
Neigh | 2.2321e-05 | 2.2321e-05 | 2.2321e-05 | 0.0 | 0.00
Comm | 0.00013151 | 0.00013151 | 0.00013151 | 0.0 | 0.00
Output | 0.00016294 | 0.00016294 | 0.00016294 | 0.0 | 0.00
Modify | 3.9779 | 3.9779 | 3.9779 | 0.0 | 99.99
Other | | 0.000173 | | | 0.00
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 77 ave 77 max 77 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 31 ave 31 max 31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31
Ave neighs/atom = 1.2916667
Ave special neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:04

4
src/MDI/Install.sh
View File

@ -57,6 +57,8 @@ include ..\/..\/lib\/mdi\/Makefile.lammps
fi
touch ../main.cpp # b/c it uses LMP_MDI
elif (test $1 = 0) then
if (test -e ../Makefile.package) then
@ -68,4 +70,6 @@ elif (test $1 = 0) then
sed -i -e '/^[ \t]*include.*mdi.*$/d' ../Makefile.package.settings
fi
touch ../main.cpp # b/c it uses LMP_MDI
fi

1
src/lammps.cpp
View File

@ -957,6 +957,7 @@ void LAMMPS::destroy()
#if defined(LMP_PLUGIN)
plugin_clear(this);
#endif
delete update;
update = nullptr;