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LATTE examples dir

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Steve Plimpton
2023-02-07 15:21:43 -07:00
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examples/QUANTUM/LATTE/README
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LATTE is a semi-empirical tight-binding quantum code, developed
primarily at Los Alamos National Labs.
# Test runs of AIMD with LAMMPS and LATTE
See these links:
Step 1: build LAMMPS
Step 2: download/build the MDI code coupling package
Step 3: download/build or install LATTE
Step 4: run the water AIMD problem for a few steps
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:
Step 1: build LAMMPS
(1) Via its LATTE package and the fix latte command
must run LAMMPS on a single processor, it calls LATTE as a library
The molecule and kspace packages are needed for the 2-water test
problem. Copy the final LAMMPS executable into the
examples/QUANTUM/PySCF directory.
(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
Traditional make:
Examples for use case (1) are in the examples/latte dir. Use case (2)
is illustrated in this dir.
% cd ~/lammps/lib/mdi
% python Install.py -m mpi
% cd ~/lammps/src
% make yes-mdi yes-molecule yes-kspace
% make -j mpi
% cp lmp_mpi ~/lammps/examples/QUANTUM/PySCF
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.
CMake:
------------------
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
% cd ~/lammps
% mkdir build; cd build
% cmake .. # includes support for all langauges (incl Fortran, Python)
% make
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes -D PKG_KSPACE=yes ../cmake
% make -j
% cp lmp ~/lammps/examples/QUANTUM/PySCF/lmp_mpi
(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
Step 2: install the MDI code coupling package
(3) Build LAMMPS with its MDI package
also with the MOLECULE package for these example scripts
(a) grab the MDI Git repo
Build with traditional make
% mkdir git; cd mdi
% git clone git@github.com:MolSSI-MDI/MDI_Library.git git
% 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
(b) build MDI
% cd mdi/git
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
% make # creates lmp
% cmake ..
% make -j
Build with CMake
(c) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find MDI:
% cd lammps
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
% make # creates lmp
For bash:
(4) Copy LAMMPS and LATTE executables into this dir
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/mdi/git"
% hash -r
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.
For (t)csh:
(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.
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git
% rehash
------------------
Notes on LATTE usage
---------------------------------
---------------------------------
You must run this version of LATTE on a single MPI processor.
However, you can use OpenMP with LATTE. To do this you need to build
LATTE with OpenMP support by editing the makefile.CHOICES file to
include -fopenmp with FFLAGS and LINKFLAGS. Also -lapack and -lblas
need to be added to LIB, and those libraries must be available on your
system. For best performance you should also build LATTE with its
PROGRESS and BML libraries. Building those libs is more complex,
see details here:
Step 3: download/build LATTE
https://github.com/lanl/LATTE_SUPER/tree/allMachines/Laptop
(a) download/build LATTE on your box
At run time, you need to also first set an environment variable for
the number of OpenMP threads to use, e.g.
NOTE: add instructions here
% export OMP_NUM_THREADS=12
(b) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find PySCF:
By default LATTE reads the latte.in file for its parameters. That
file specifies other files LATTE will read. With MDI, the driver code
(e.g. LAMMPS) can use the >FNAME command to specify an alternate
filename to use instead of latte.in.
For bash:
By default LATTE writes out a log.latte file with info about its
calculations. An "OUTFILE= logfile" setting in latte.in can rename
this file.
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/pyscf/git"
% hash -r
---------
Run example #1: AIMD
For (t)csh:
* Run with MPI: 1 proc each
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/pyscf/git
% rehash
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"
(c) Check that you can import the 4 Python modules which the script
that wraps PySCF will need:
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
% python
>>> import numpy as np
>>> from mpi4py import MPI
>>> import MDI_Library as mdi
>>> import pyscf
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
Step 4: run the water AIMD problem for a few steps
lmp_mpi -mdi \
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
-in in.aimd.plugin -log log.aimd.lammps.plugin
% cd ~/lammps/examples/QUANTUM/LATTE
NOTE: The -plugin_path needs to point to where LATTE was built in step
(2).
# Run with TCP: 1 proc each
---------
Run example #2: sequence of configurations
% lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.tcp.1 -in in.water &
* Run with MPI: 1 proc each
% python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.water
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: 1 proc each
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
% 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 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
* 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.plugin.1 -in in.water.plugin
lmp_mpi -mdi \
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
-in in.series.plugin -log log.series.lammps.plugin
---------------------------------
---------------------------------
NOTE: The -plugin_path needs to point to where LATTE was built in step
(2).
Step 5: run the UO2 AIMD problem for a few steps
% cd ~/lammps/examples/QUANTUM/LATTE
# Run with TCP: 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
# Run with MPI: 1 proc each
% 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
# 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.uo2.plugin.1 -in in.uo2.plugin
---------------------------------
---------------------------------
Step 6: run the UO2 series problem
% cd ~/lammps/examples/QUANTUM/LATTE
# 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

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# Test runs of AIMD with LAMMPS and LATTE
Step 1: build LAMMPS
Step 2: download/build the MDI code coupling package
Step 3: download/build or install LATTE
Step 4: run the water AIMD problem for a few steps
---------------------------------
---------------------------------
Step 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.
Traditional make:
% cd ~/lammps/lib/mdi
% python Install.py -m mpi
% cd ~/lammps/src
% make yes-mdi yes-molecule yes-kspace
% make -j mpi
% cp lmp_mpi ~/lammps/examples/QUANTUM/PySCF
CMake:
% cd ~/lammps
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes -D PKG_KSPACE=yes ../cmake
% make -j
% cp lmp ~/lammps/examples/QUANTUM/PySCF/lmp_mpi
---------------------------------
---------------------------------
Step 2: install the MDI code coupling package
(a) grab the MDI Git repo
% mkdir git; cd mdi
% git clone git@github.com:MolSSI-MDI/MDI_Library.git git
(b) build MDI
% cd mdi/git
% mkdir build; cd build
% cmake ..
% make -j
(c) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find MDI:
For bash:
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/mdi/git"
% hash -r
For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git
% rehash
---------------------------------
---------------------------------
Step 3: install PySCF
(a) download/build or install PySCF on your box
NOTE: add instructions here
(b) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find PySCF:
For bash:
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/pyscf/git"
% hash -r
For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/pyscf/git
% 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
% cd ~/lammps/examples/QUANTUM/LATTE
# Run with TCP: 1 proc each
% lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.latte.aimd.tcp.1 -in in.water.latte.aimd &
% python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.water
# Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.latte.aimd.mpi.1 -in in.water.latte.aimd : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.water
# 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.latte.aimd.plugin.1 -in in.water.latte.aimd.plugin
---------------------------------
---------------------------------
Step 5: run the UO2 AIMD problem for a few steps
% cd ~/lammps/examples/QUANTUM/LATTE
# Run with TCP: 1 proc each
% lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.uo2.latte.aimd.tcp.1 -in in.uo2.latte.aimd &
% 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.uo2.latte.aimd.mpi.1 -in in.uo2.latte.aimd : -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.uo2.latte.aimd.plugin.1 -in in.uo2.latte.aimd.plugin
---------------------------------
---------------------------------
Step 6: run the UO2 series problem
% cd ~/lammps/examples/QUANTUM/LATTE
# Run with TCP: 1 proc each
% lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.uo2.latte.series.tcp.1 -in in.uo2.latte.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.uo2.latte.series.mpi.1 -in in.uo2.latte.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.uo2.latte.series.plugin.1 -in in.uo2.latte.series.plugin

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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

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@ -1,315 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.7 2.7 0 -0.601491 0.335597 -0.87242 -2.27066e-14 -1.33391e-14 2.31141e-14
2 2 1.35 4.05 1.35 8.2897 4.55901 5.97376 2.35473 2.21578e-14 7.40069e-15
3 2 4.05 4.05 1.35 1.7742 6.51885 0.385522 -2.35473 2.97071e-15 -2.01341e-14
4 1 2.7 1.65327e-16 2.7 -0.325605 -1.03244 0.724324 -2.90278e-14 6.77422e-15 2.86766e-15
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3 2 4.05107 4.05652 1.35039 0.361248 6.51586 0.386144 -2.32753 -0.00987687 0.00204727
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3 2 4.05073 4.06303 1.35077 -1.03064 6.50691 0.387927 -2.28482 -0.0198564 0.00378025
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6 2 4.04593 1.35272 4.04391 -3.60334 0.765381 -1.74213 -2.26667 -0.0176868 -0.00261028
ITEM: TIMESTEP
15
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69775 2.70126 -0.0032738 -0.596036 0.339698 -0.874275 0.0733392 0.0523895 -0.0260413
2 2 1.39074 4.06704 1.37236 13.3225 4.51268 5.93571 2.05037 -0.0469451 -0.0384133
3 2 4.04685 4.07439 1.35146 -3.3869 6.47632 0.392716 -2.17093 -0.038409 0.00471919
4 1 2.69879 -0.00386739 2.70272 -0.319232 -1.02877 0.727309 0.0912666 0.0549279 0.0456036
5 2 1.36896 1.3444 4.04096 7.63043 -1.49619 -2.3986 2.20924 -0.00309551 0.0168709
6 2 4.04498 1.35291 4.04347 -3.94416 0.762625 -1.74253 -2.25329 -0.0188678 -0.0027391
ITEM: TIMESTEP
16
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.6976 2.70135 -0.00349241 -0.595266 0.340245 -0.87455 0.0787153 0.055569 -0.0281032
2 2 1.39411 4.06817 1.37384 13.6294 4.50526 5.92964 2.02007 -0.0514799 -0.042077
3 2 4.04596 4.07601 1.35155 -3.71274 6.47031 0.393413 -2.15039 -0.0412405 0.00452364
4 1 2.69871 -0.00412452 2.7029 -0.318268 -1.02819 0.727794 0.0990893 0.0601283 0.0501398
5 2 1.37091 1.34403 4.04036 7.96225 -1.49665 -2.39594 2.19142 -0.00294819 0.0183708
6 2 4.04395 1.3531 4.04304 -4.28288 0.759692 -1.74296 -2.2389 -0.0200287 -0.00285406
ITEM: TIMESTEP
17
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69745 2.70143 -0.00371108 -0.594441 0.340824 -0.874845 0.0841889 0.0587168 -0.0301987
2 2 1.39755 4.0693 1.37532 13.9317 4.49714 5.92301 1.9884 -0.0562187 -0.0458954
3 2 4.04499 4.07763 1.35165 -4.0354 6.46388 0.394073 -2.12872 -0.0441293 0.0042247
4 1 2.69863 -0.00438149 2.70308 -0.317223 -1.02755 0.728326 0.107162 0.0655439 0.054894
5 2 1.37294 1.34365 4.03976 8.2913 -1.49708 -2.39305 2.17248 -0.00274479 0.0199293
6 2 4.04284 1.35329 4.0426 -4.61936 0.756586 -1.74339 -2.2235 -0.0211679 -0.00295392
ITEM: TIMESTEP
18
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69731 2.70152 -0.00392983 -0.593559 0.341435 -0.875162 0.0897661 0.0618346 -0.0323262
2 2 1.40107 4.07042 1.3768 14.229 4.48829 5.91578 1.95532 -0.0611659 -0.0498706
3 2 4.04394 4.07924 1.35175 -4.3547 6.457 0.394679 -2.10593 -0.0470792 0.0038154
4 1 2.69855 -0.00463829 2.70327 -0.316095 -1.02686 0.728907 0.11549 0.0711775 0.0598705
5 2 1.37506 1.34328 4.03916 8.61741 -1.49747 -2.38993 2.15241 -0.00248344 0.0215483
6 2 4.04164 1.35348 4.04217 -4.95344 0.753309 -1.74385 -2.20706 -0.0222835 -0.00303744
ITEM: TIMESTEP
19
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69716 2.7016 -0.00414866 -0.592621 0.342077 -0.8755 0.0954526 0.0649239 -0.0344841
2 2 1.40467 4.07154 1.37828 14.5213 4.47868 5.90795 1.92083 -0.0663258 -0.0540045
3 2 4.04281 4.08086 1.35185 -4.67049 6.44967 0.395215 -2.08198 -0.050094 0.00328881
4 1 2.69847 -0.00489492 2.70345 -0.314881 -1.02611 0.72954 0.124076 0.0770317 0.0650736
5 2 1.37725 1.3429 4.03857 8.94041 -1.49782 -2.38655 2.13119 -0.00216234 0.0232295
6 2 4.04036 1.35367 4.04173 -5.28496 0.749867 -1.74431 -2.18956 -0.0233735 -0.00310338
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69701 2.70169 -0.00436758 -0.591624 0.342751 -0.875861 0.101254 0.0679866 -0.0366705
2 2 1.40833 4.07266 1.37976 14.8083 4.46827 5.89948 1.88489 -0.0717024 -0.0582989
3 2 4.0416 4.08247 1.35195 -4.98257 6.44189 0.395662 -2.05686 -0.0531772 0.00263798
4 1 2.69839 -0.00515135 2.70363 -0.313579 -1.0253 0.730227 0.132925 0.0831089 0.0705072
5 2 1.37953 1.34253 4.03797 9.26012 -1.49812 -2.38291 2.1088 -0.00177977 0.0249746
6 2 4.039 1.35386 4.04129 -5.61376 0.746262 -1.74478 -2.171 -0.0244362 -0.00315046

15
examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.1.2uo2
View File

@ -1,15 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 2.7 0 -2.27066e-14 -1.33391e-14 2.31141e-14
2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14

18
examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.1.3uo2
View File

@ -1,18 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
9
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.6199999999999999e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 2.7 0 -1.27436e-13 0.760572 0.760572
2 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
3 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901

21
examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.1.4uo2
View File

@ -1,21 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
12
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
10 1 5.4 0 0 0.211437 1.63064 -0.0728897
11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959

15
examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.2uo2
View File

@ -1,15 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 2.7 0 -2.27066e-14 -1.33391e-14 2.31141e-14
2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14

18
examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.3uo2
View File

@ -1,18 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
9
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.6199999999999999e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 2.7 0 -1.27436e-13 0.760572 0.760572
2 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
3 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901

21
examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.4uo2
View File

@ -1,21 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
12
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
10 1 5.4 0 0 0.211437 1.63064 -0.0728897
11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959

15
examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.2uo2
View File

@ -1,15 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 2.7 0 -2.27066e-14 -1.33391e-14 2.31141e-14
2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14

18
examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.3uo2
View File

@ -1,18 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
9
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.6199999999999999e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 2.7 0 -1.27436e-13 0.760572 0.760572
2 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
3 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901

21
examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.4uo2
View File

@ -1,21 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
12
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
10 1 5.4 0 0 0.211437 1.63064 -0.0728897
11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959

26
examples/QUANTUM/LATTE/in.aimd
View File

@ -1,26 +0,0 @@
# 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 2uo2.lmp
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 92 8
thermo_style custom step temp pe etotal press
thermo 1
#dump 1 all custom 1 dump.aimd.mpi &
# id type x y z vx vy vz fx fy fz
run 20

27
examples/QUANTUM/LATTE/in.aimd.plugin
View File

@ -1,27 +0,0 @@
# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
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 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.plugin &
id type x y z vx vy vz fx fy fz
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
command "run 20"

40
examples/QUANTUM/LATTE/in.latte.water.md
View File

@ -1,40 +0,0 @@
# simple water model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water.latte.aimd
# 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 latte
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 100

8
examples/QUANTUM/LATTE/in.series
View File

@ -11,22 +11,22 @@ label LOOP
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data data.${files}
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
fix 1 all mdi/qm virial yes elements U O connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
write_dump all custom dump.series.mpi.${files} &
id type x y z fx fy fz modify sort id
#write_dump all custom dump.series.mpi.${files} &
# id type x y z fx fy fz modify sort id
clear

13
examples/QUANTUM/LATTE/in.series.plugin
View File

@ -9,21 +9,22 @@ label LOOP
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data data.${files}
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements 92 8
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" &
command "run 0"
extra latte.in.uo2 command "run 0"
write_dump all custom dump.series.plugin.${files} &
id type x y z fx fy fz modify sort id
#write_dump all custom dump.series.plugin.${files} &
# id type x y z fx fy fz modify sort id
clear

2
examples/QUANTUM/LATTE/in.uo2.latte.aimd → examples/QUANTUM/LATTE/in.uo2
View File

@ -4,7 +4,7 @@ units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
read_data data.2uo2
velocity all create 300.0 87287 loop geom

37
examples/QUANTUM/LATTE/in.uo2.latte.series
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@ -1,37 +0,0 @@
# 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
atom_modify sort 0 0.0
read_data ${files}.lmp
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements U O connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
write_dump all custom dump.series.mpi.${files} &
id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP
mdi exit

32
examples/QUANTUM/LATTE/in.uo2.latte.series.plugin
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@ -1,32 +0,0 @@
# 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
atom_modify sort 0 0.0
read_data ${files}.lmp
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements U O
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
extra latte.in.uo2 command "run 0"
write_dump all custom dump.series.plugin.${files} &
id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP

2
examples/QUANTUM/LATTE/in.uo2.latte.aimd.plugin → examples/QUANTUM/LATTE/in.uo2.plugin
View File

@ -4,7 +4,7 @@ units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
read_data data.2uo2
velocity all create 300.0 87287 loop geom

2
examples/QUANTUM/LATTE/in.water.latte.aimd → examples/QUANTUM/LATTE/in.water
View File

@ -4,7 +4,7 @@ units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water.latte.aimd
read_data data.water
# replicate system if requested

2
examples/QUANTUM/LATTE/in.water.latte.aimd.plugin → examples/QUANTUM/LATTE/in.water.plugin
View File

@ -4,7 +4,7 @@ units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water.latte.aimd
read_data data.water
# replicate system if requested