From 2cd32d7e76e8fa1695a61913eab35f715699f8ef Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 8 Feb 2023 12:54:34 -0700 Subject: [PATCH] clean up --- examples/QUANTUM/QE/README | 63 -------------- examples/QUANTUM/QE/data.water.qe.aimd | 92 --------------------- examples/QUANTUM/QE/in.qe.water | 63 -------------- examples/QUANTUM/QE/in.water.qe.aimd | 38 --------- examples/QUANTUM/QE/in.water.qe.aimd.plugin | 40 --------- examples/QUANTUM/README | 10 +-- examples/README | 2 +- 7 files changed, 6 insertions(+), 302 deletions(-) delete mode 100644 examples/QUANTUM/QE/README delete mode 100644 examples/QUANTUM/QE/data.water.qe.aimd delete mode 100644 examples/QUANTUM/QE/in.qe.water delete mode 100644 examples/QUANTUM/QE/in.water.qe.aimd delete mode 100644 examples/QUANTUM/QE/in.water.qe.aimd.plugin diff --git a/examples/QUANTUM/QE/README b/examples/QUANTUM/QE/README deleted file mode 100644 index 4ebdff5ef9..0000000000 --- a/examples/QUANTUM/QE/README +++ /dev/null @@ -1,63 +0,0 @@ -# Test runs of QMMM with LAMMPS and Quantum Espress (QE) - -Step 1: build LAMMPS -Step 2: download/build QE with MDI support -Step 3: run test problem - ---------------------------------- ---------------------------------- - -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/QE - -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/QE/lmp_mpi - ---------------------------------- ---------------------------------- - -Step 2: download/build QE with MDI support - -% git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git -% cd qe/git -% ./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" try_foxflags="-fPIC -cpp" -% make mdi - -copy MDI/src/qemdi.x to QUANTUM/QE - ---------------------------------- ---------------------------------- - -Step 3: run test problem - -% cd ~/lammps/examples/QUANTUM/QE - -# Run with TCP: 1 proc each - -% mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.test.qe.aimd.tcp.1 -in in.water.qe.aimd & -% qemdi.x -in in.qe.test -mdi "-name QE -role ENGINE -method TCP -port 8021 -hostname localhost" - -# Run with MPI: 1 proc each - -% mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.test.qe.aimd.mpi.1 -in in.water.qe.aimd : -np 1 qemdi.x -in in.qe.test -mdi "-name QE -role ENGINE -method MPI" - -# Run in plugin mode: 1 proc - -% mpirun -np 1 lmp_mpi -mdi "-role DRIVER -name driver -method LINK -plugin_path /home/sjplimp/qe/git/MDI/src" -log log.test.qe.aimd.plugin.1 -in in.test.qe.aimd.plugin diff --git a/examples/QUANTUM/QE/data.water.qe.aimd b/examples/QUANTUM/QE/data.water.qe.aimd deleted file mode 100644 index 21e8e6c5c8..0000000000 --- a/examples/QUANTUM/QE/data.water.qe.aimd +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS data file for water - -24 atoms -16 bonds -8 angles -0 dihedrals -0 impropers - -2 atom types -1 bond types -1 angle types -0 dihedral types -0 improper types - -0.0 4.9325 xlo xhi -0.0 4.9325 ylo yhi -0.0 4.9325 zlo zhi - -Masses - -1 15.9994 -2 1.008 - -Pair Coeffs - -1 0.102 3.188 -2 0.000 0.000 - -Bond Coeffs - -1 450 0.9572 - -Angle Coeffs - -1 55.0 104.52 - -Atoms - -1 0 1 -0.83400 2.17919 0.196156 4.15513 -2 0 2 0.41700 2.29785 4.8353 0.126003 -3 0 2 0.41700 1.82037 1.07996 4.23498 -4 0 1 -0.83400 4.65839 0.120414 0.305758 -5 0 2 0.41700 4.67446 -0.0220991 4.29186 -6 0 2 0.41700 4.28188 0.994196 0.410515 -7 0 1 -0.83400 3.65045 2.40907 0.344349 -8 0 2 0.41700 3.52052 2.1838 4.35565 -9 0 2 0.41700 4.26579 3.14208 0.327669 -10 0 1 -0.83400 1.21327 2.62177 4.15519 -11 0 2 0.41700 1.47452 3.53837 4.0667 -12 0 2 0.41700 1.20743 2.46396 0.16677 -13 0 1 -0.83400 4.45777 4.47325 2.74192 -14 0 2 0.41700 4.53396 4.49652 1.78804 -15 0 2 0.41700 4.21354 3.56943 2.94119 -16 0 1 -0.83400 2.04119 4.41585 1.64725 -17 0 2 0.41700 2.26934 4.77582 2.50434 -18 0 2 0.41700 1.69079 3.54574 1.83793 -19 0 1 -0.83400 3.73384 1.97964 2.81949 -20 0 2 0.41700 3.41083 2.22014 1.95113 -21 0 2 0.41700 3.91914 1.04272 2.75561 -22 0 1 -0.83400 1.20859 2.09853 1.68186 -23 0 2 0.41700 1.01865 2.25693 2.60655 -24 0 2 0.41700 1.16884 1.14674 1.58832 - -Bonds - -1 1 1 2 -2 1 1 3 -3 1 4 5 -4 1 4 6 -5 1 7 8 -6 1 7 9 -7 1 10 11 -8 1 10 12 -9 1 13 14 -10 1 13 15 -11 1 16 17 -12 1 16 18 -13 1 19 20 -14 1 19 21 -15 1 22 23 -16 1 22 24 - -Angles - -1 1 2 1 3 -2 1 5 4 6 -3 1 8 7 9 -4 1 11 10 12 -5 1 14 13 15 -6 1 17 16 18 -7 1 20 19 21 -8 1 23 22 24 diff --git a/examples/QUANTUM/QE/in.qe.water b/examples/QUANTUM/QE/in.qe.water deleted file mode 100644 index 61e23688e9..0000000000 --- a/examples/QUANTUM/QE/in.qe.water +++ /dev/null @@ -1,63 +0,0 @@ -&CONTROL -title="Test" -calculation='md', -restart_mode = 'from_scratch', -tprnfor=.t., -prefix='qe', -pseudo_dir='pseudo' -nstep = 1, -tqmmm = .true. -/ - -&SYSTEM -ibrav = 1, -celldm(1) = 9.321077825, -celldm(2) = 1., -celldm(3) = 1., -celldm(4) = 0., -celldm(5) = 0., -celldm(6) = 0., -nat = 24, -ntyp = 2, -ecutwfc = 80.0 , -/ - -&ELECTRONS -conv_thr = 1.D-6, -/ - -&IONS -ion_positions = 'default' -/ - -ATOMIC_SPECIES -O 16.0000 O.pbe-van_bm.UPF -H 1.0000 H.pbe-van_ak.UPF - -ATOMIC_POSITIONS angstrom -O 2.17919 0.196156 4.15513 -H 2.29785 4.8353 0.126003 -H 1.82037 1.07996 4.23498 -O 4.65839 0.120414 0.305758 -H 4.67446 -0.0220991 4.29186 -H 4.28188 0.994196 0.410515 -O 3.65045 2.40907 0.344349 -H 3.52052 2.1838 4.35565 -H 4.26579 3.14208 0.327669 -O 1.21327 2.62177 4.15519 -H 1.47452 3.53837 4.0667 -H 1.20743 2.46396 0.16677 -O 4.45777 4.47325 2.74192 -H 4.53396 4.49652 1.78804 -H 4.21354 3.56943 2.94119 -O 2.04119 4.41585 1.64725 -H 2.26934 4.77582 2.50434 -H 1.69079 3.54574 1.83793 -O 3.73384 1.97964 2.81949 -H 3.41083 2.22014 1.95113 -H 3.91914 1.04272 2.75561 -O 1.20859 2.09853 1.68186 -H 1.01865 2.25693 2.60655 -H 1.16884 1.14674 1.58832 - -K_POINTS gamma diff --git a/examples/QUANTUM/QE/in.water.qe.aimd b/examples/QUANTUM/QE/in.water.qe.aimd deleted file mode 100644 index dbd339f88c..0000000000 --- a/examples/QUANTUM/QE/in.water.qe.aimd +++ /dev/null @@ -1,38 +0,0 @@ -# AIMD for water with LAMMPS + QE - -units real -neigh_modify delay 0 every 1 check yes -atom_style full -bond_style harmonic -angle_style harmonic -pair_style lj/cut/coul/long 10.0 -pair_modify mix arithmetic -kspace_style pppm 1e-4 -special_bonds amber - -atom_modify sort 0 0 - -read_data data.water.qe.aimd - -timestep 1.0 - -#dump 1 all custom 1 dump.lammpstrj id element xu yu zu -#dump 2 all custom 1 dump.force id element fx fy fz -#dump 3 all xyz 1 dump.xyz -#dump_modify 1 element O H -#dump_modify 2 element O H - -thermo_style multi -thermo 1 - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/qm virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -run 5 diff --git a/examples/QUANTUM/QE/in.water.qe.aimd.plugin b/examples/QUANTUM/QE/in.water.qe.aimd.plugin deleted file mode 100644 index 6d17b08a97..0000000000 --- a/examples/QUANTUM/QE/in.water.qe.aimd.plugin +++ /dev/null @@ -1,40 +0,0 @@ -# AIMD for water with LAMMPS + QE - -units real -neigh_modify delay 0 every 1 check yes -atom_style full -bond_style harmonic -angle_style harmonic -pair_style lj/cut/coul/long 10.0 -pair_modify mix arithmetic -kspace_style pppm 1e-4 -special_bonds amber - -atom_modify sort 0 0 - -read_data lammps.data - -timestep 1.0 - -#dump 1 all custom 1 dump.lammpstrj id element xu yu zu -#dump 2 all custom 1 dump.force id element fx fy fz -#dump 3 all xyz 1 dump.xyz -#dump_modify 1 element O H -#dump_modify 2 element O H - -thermo_style multi -thermo 1 - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/qm virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -mdi plugin qemdi mdi "-role ENGINE -name QE -method LINK" & - extra "--in qe.in" & - command "run 5" diff --git a/examples/QUANTUM/README b/examples/QUANTUM/README index 7cc837423f..6a795e2134 100644 --- a/examples/QUANTUM/README +++ b/examples/QUANTUM/README @@ -5,20 +5,20 @@ LATTE = semi-empirical tight-binding code from LANL https://www.osti.gov/biblio/1526907-los-alamos-transferable-tight-binding-energetics-latte-version https://github.com/lanl/LATTE -PySCF = ??? from Caltech - add link - NWChem = computational chemistry code from PNNL focus here is on DFT portion of NWChem = PWDFT library https://www.nwchem-sw.org -Quantum Espresso (QE) = DFT code for materials modeling - https://www.quantum-espresso.org/ +PySCF = quantum chemistry code from Caltech + https://pyscf.org/index.html ----------------------------------------------------- To be added later (as of Feb 2023): +Quantum Espresso (QE) = DFT code for materials modeling + https://www.quantum-espresso.org + DFT-FE = real-space DFT code from U Michigan https://github.com/dftfeDevelopers/dftfe diff --git a/examples/README b/examples/README index 8a12d3fae4..bb4c6e759c 100644 --- a/examples/README +++ b/examples/README @@ -191,7 +191,7 @@ https://docs.lammps.org/Build_package.html page for more info about installing and building packages. The QUANTUM directory has examples of how to use LAMMPS in tandem with -several quantum codes. +several quantum codes via the MDI code coupling library. The TIP4P directory has an example for testing forces computed on a GPU.