diff --git a/examples/QUANTUM/LATTE/README b/examples/QUANTUM/LATTE/README index 8ab40c9c65..072210342f 100644 --- a/examples/QUANTUM/LATTE/README +++ b/examples/QUANTUM/LATTE/README @@ -1,161 +1,156 @@ -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 diff --git a/examples/QUANTUM/LATTE/README.new b/examples/QUANTUM/LATTE/README.new deleted file mode 100644 index 1fae90633d..0000000000 --- a/examples/QUANTUM/LATTE/README.new +++ /dev/null @@ -1,156 +0,0 @@ -# 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 diff --git a/examples/QUANTUM/LATTE/README.old b/examples/QUANTUM/LATTE/README.old new file mode 100644 index 0000000000..4636f7c60b --- /dev/null +++ b/examples/QUANTUM/LATTE/README.old @@ -0,0 +1,179 @@ +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 diff --git a/examples/QUANTUM/LATTE/2uo2.lmp b/examples/QUANTUM/LATTE/data.2uo2 similarity index 100% rename from examples/QUANTUM/LATTE/2uo2.lmp rename to examples/QUANTUM/LATTE/data.2uo2 diff --git a/examples/QUANTUM/LATTE/3uo2.lmp b/examples/QUANTUM/LATTE/data.3uo2 similarity index 100% rename from examples/QUANTUM/LATTE/3uo2.lmp rename to examples/QUANTUM/LATTE/data.3uo2 diff --git a/examples/QUANTUM/LATTE/4uo2.lmp b/examples/QUANTUM/LATTE/data.4uo2 similarity index 100% rename from examples/QUANTUM/LATTE/4uo2.lmp rename to examples/QUANTUM/LATTE/data.4uo2 diff --git a/examples/QUANTUM/LATTE/data.water.latte.aimd b/examples/QUANTUM/LATTE/data.water similarity index 100% rename from examples/QUANTUM/LATTE/data.water.latte.aimd rename to examples/QUANTUM/LATTE/data.water diff --git a/examples/QUANTUM/LATTE/dump.8Sep22.aimd.mpi.1 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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 diff --git a/examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.2uo2 b/examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.2uo2 deleted file mode 100644 index a44cbc396e..0000000000 --- a/examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.2uo2 +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.3uo2 b/examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.3uo2 deleted file mode 100644 index 1a275b6e18..0000000000 --- a/examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.3uo2 +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.4uo2 b/examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.4uo2 deleted file mode 100644 index 3b9e4eeb3f..0000000000 --- a/examples/QUANTUM/LATTE/dump.8Sep22.series.mpi.2.4uo2 +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.2uo2 b/examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.2uo2 deleted file mode 100644 index a44cbc396e..0000000000 --- a/examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.2uo2 +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.3uo2 b/examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.3uo2 deleted file mode 100644 index 1a275b6e18..0000000000 --- a/examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.3uo2 +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.4uo2 b/examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.4uo2 deleted file mode 100644 index 3b9e4eeb3f..0000000000 --- a/examples/QUANTUM/LATTE/dump.8Sep22.series.plugin.4uo2 +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/in.aimd b/examples/QUANTUM/LATTE/in.aimd deleted file mode 100644 index 3c713dfdc6..0000000000 --- a/examples/QUANTUM/LATTE/in.aimd +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/in.aimd.plugin b/examples/QUANTUM/LATTE/in.aimd.plugin deleted file mode 100644 index a485cb671a..0000000000 --- a/examples/QUANTUM/LATTE/in.aimd.plugin +++ /dev/null @@ -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" diff --git a/examples/QUANTUM/LATTE/in.latte.water.md b/examples/QUANTUM/LATTE/in.latte.water.md deleted file mode 100644 index 1d2ea7eecb..0000000000 --- a/examples/QUANTUM/LATTE/in.latte.water.md +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/in.series b/examples/QUANTUM/LATTE/in.series index ac383b53a2..734dc9fa94 100644 --- a/examples/QUANTUM/LATTE/in.series +++ b/examples/QUANTUM/LATTE/in.series @@ -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 diff --git a/examples/QUANTUM/LATTE/in.series.plugin b/examples/QUANTUM/LATTE/in.series.plugin index 0985503746..5219a9de37 100644 --- a/examples/QUANTUM/LATTE/in.series.plugin +++ b/examples/QUANTUM/LATTE/in.series.plugin @@ -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 diff --git a/examples/QUANTUM/LATTE/in.uo2.latte.aimd b/examples/QUANTUM/LATTE/in.uo2 similarity index 95% rename from examples/QUANTUM/LATTE/in.uo2.latte.aimd rename to examples/QUANTUM/LATTE/in.uo2 index 86dde9c3e0..b4920b391c 100644 --- a/examples/QUANTUM/LATTE/in.uo2.latte.aimd +++ b/examples/QUANTUM/LATTE/in.uo2 @@ -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 diff --git a/examples/QUANTUM/LATTE/in.uo2.latte.series b/examples/QUANTUM/LATTE/in.uo2.latte.series deleted file mode 100644 index 578ee62282..0000000000 --- a/examples/QUANTUM/LATTE/in.uo2.latte.series +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/in.uo2.latte.series.plugin b/examples/QUANTUM/LATTE/in.uo2.latte.series.plugin deleted file mode 100644 index 0654c9c12e..0000000000 --- a/examples/QUANTUM/LATTE/in.uo2.latte.series.plugin +++ /dev/null @@ -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 diff --git a/examples/QUANTUM/LATTE/in.uo2.latte.aimd.plugin b/examples/QUANTUM/LATTE/in.uo2.plugin similarity index 96% rename from examples/QUANTUM/LATTE/in.uo2.latte.aimd.plugin rename to examples/QUANTUM/LATTE/in.uo2.plugin index e17b34c1d3..02f6f4d415 100644 --- a/examples/QUANTUM/LATTE/in.uo2.latte.aimd.plugin +++ b/examples/QUANTUM/LATTE/in.uo2.plugin @@ -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 diff --git a/examples/QUANTUM/LATTE/in.water.latte.aimd b/examples/QUANTUM/LATTE/in.water similarity index 95% rename from examples/QUANTUM/LATTE/in.water.latte.aimd rename to examples/QUANTUM/LATTE/in.water index 56f3f78692..ed26a87553 100644 --- a/examples/QUANTUM/LATTE/in.water.latte.aimd +++ b/examples/QUANTUM/LATTE/in.water @@ -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 diff --git a/examples/QUANTUM/LATTE/in.water.latte.aimd.plugin b/examples/QUANTUM/LATTE/in.water.plugin similarity index 95% rename from examples/QUANTUM/LATTE/in.water.latte.aimd.plugin rename to examples/QUANTUM/LATTE/in.water.plugin index 310ccc9512..db388deee1 100644 --- a/examples/QUANTUM/LATTE/in.water.latte.aimd.plugin +++ b/examples/QUANTUM/LATTE/in.water.plugin @@ -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