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clean up

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This commit is contained in:
Steve Plimpton
2023-02-08 12:54:34 -07:00
parent 10b20ec647
commit 2cd32d7e76
7 changed files with 6 additions and 302 deletions
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63
examples/QUANTUM/QE/README
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# 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

92
examples/QUANTUM/QE/data.water.qe.aimd
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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

63
examples/QUANTUM/QE/in.qe.water
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&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

38
examples/QUANTUM/QE/in.water.qe.aimd
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# 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

40
examples/QUANTUM/QE/in.water.qe.aimd.plugin
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# 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"

10
examples/QUANTUM/README
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@ -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

2
examples/README
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@ -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.