Adding LAMMPS backend

examples/README.md

@@ -50,6 +50,7 @@ Examples for Methods using OpenMM can be found in the subfolder [openmm](openmm)
 ## Installation of the Environment
 
 We have a Google Colab that shows how the MD engines and PySAGES can be installed together as a guide to install PySAGES.
+
 This notebook has a final step that sets up precompiled environments for all the other notebooks as well.
 [![Install Env](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/Install_PySAGES_Environment.ipynb)
 

examples/hoomd-blue/harmonic_bias/harmonic_bias.py

@@ -39,6 +39,7 @@ def validate_hist(xi_hist, target, epsilon=0.1):
 def get_target_dist(center, k, lim, bins):
     x = np.linspace(lim[0], lim[1], bins)
     p = np.exp(-0.5 * k * (x - center) ** 2)
+
     # norm numerically
     p *= (lim[1] - lim[0]) / np.sum(p)
     return p
@@ -55,6 +56,7 @@ def generate_context(**kwargs):
         nl = hoomd.md.nlist.cell()
         dpd = hoomd.md.pair.dpd(r_cut=1, nlist=nl, seed=42, kT=1.0)
         dpd.pair_coeff.set("A", "A", A=kwargs.get("A", 5.0), gamma=kwargs.get("gamma", 1.0))
+
     return context
 
 

examples/hoomd-blue/umbrella_integration/integration.py

@@ -64,6 +64,7 @@ def plot_hist(result, bins=50):
                     ax[x, y].plot(edges, histo, label=f"center {center}")
                     ax[x, y].legend(loc="best", fontsize="xx-small")
                     ax[x, y].set_yscale("log")
+
             counter += hist_per
     while counter < len(result["centers"]):
         center = np.asarray(result["centers"][counter])

examples/lammps/unbiased/in.lj

@@ -0,0 +1,30 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100

examples/lammps/unbiased/log.lammps.8Feb2023

@@ -0,0 +1,160 @@
+LAMMPS (8 Feb 2023)
+KOKKOS mode is enabled (src/KOKKOS/kokkos.cpp:106)
+  will use up to 1 GPU(s) per node
+package kokkos
+# 3d Lennard-Jones melt
+
+
+
+variable	x index 1
+
+variable	y index 1
+
+variable	z index 1
+
+
+
+variable	xx equal 20*$x
+
+variable	xx equal 20*1
+
+variable	yy equal 20*$y
+
+variable	yy equal 20*1
+
+variable	zz equal 20*$z
+
+variable	zz equal 20*1
+
+
+
+units		lj
+
+atom_style	atomic
+
+
+
+lattice		fcc 0.8442
+
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+
+region		box block 0 20 0 ${yy} 0 ${zz}
+
+region		box block 0 20 0 20 0 ${zz}
+
+region		box block 0 20 0 20 0 20
+
+create_box	1 box
+
+Created orthogonal box = (0 0 0) to (33.591924 33.591924 33.591924)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+
+Created 32000 atoms
+  using lattice units in orthogonal box = (0 0 0) to (33.591924 33.591924 33.591924)
+  create_atoms CPU = 0.005 seconds
+mass		1 1.0
+
+
+
+velocity	all create 1.44 87287 loop geom
+
+
+
+pair_style	lj/cut 2.5
+
+pair_coeff	1 1 1.0 1.0 2.5
+
+
+
+neighbor	0.3 bin
+
+neigh_modify	delay 0 every 20 check no
+
+
+
+fix		1 all nve
+
+
+
+run		100
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 20 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 2.8, bins = 12 12 12
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/kk, perpetual
+      attributes: full, newton off, kokkos_device
+      pair build: full/bin/kk/device
+      stencil: full/bin/3d
+      bin: kk/device
+Per MPI rank memory allocation (min/avg/max) = 7.475 | 7.475 | 7.475 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.44          -6.7733681      0             -4.6134356     -5.0197073    
+       100   0.7574531     -5.7585055      0             -4.6223613      0.20726105   
+Loop time of 0.0285314 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 1514122.080 tau/day, 3504.912 timesteps/s, 112.157 Matom-step/s
+95.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.001557   | 0.001557   | 0.001557   |   0.0 |  5.46
+Neigh   | 0.0051532  | 0.0051532  | 0.0051532  |   0.0 | 18.06
+Comm    | 0.0032644  | 0.0032644  | 0.0032644  |   0.0 | 11.44
+Output  | 4.0139e-05 | 4.0139e-05 | 4.0139e-05 |   0.0 |  0.14
+Modify  | 0.017342   | 0.017342   | 0.017342   |   0.0 | 60.78
+Other   |            | 0.001175   |            |       |  4.12
+
+Nlocal:          32000 ave       32000 max       32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          19657 ave       19657 max       19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2405666
+Ave neighs/atom = 75.177063
+Neighbor list builds = 5
+Dangerous builds not checked
+run 0
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.556 | 7.556 | 7.556 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+       100   0.7574531     -5.7585055      0             -4.6223613      0.20726105   
+Loop time of 0.00049331 on 1 procs for 0 steps with 32000 atoms
+
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.0004933  |            |       |100.00
+
+Nlocal:          32000 ave       32000 max       32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          19657 ave       19657 max       19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2405666
+Ave neighs/atom = 75.177063
+Neighbor list builds = 0
+Dangerous builds not checked
+Total wall time: 0:00:00

examples/lammps/unbiased/simple.py

@@ -0,0 +1,110 @@
+#!/usr/bin/env python3
+# preceding line should have path for Python on your machine
+#
+# simple.py
+# Serial syntax: ./simple.py in.lj
+#                in.lj = LAMMPS input script
+#
+# LAMMPS build with the following configuration to enable the KOKKOS and PYTHON packages:
+# ccmake -S cmake -B build -D PKG_KOKKOS=on -D Kokkos_ENABLE_CUDA=on -D Kokkos_ARCH_AMPERE80=on \
+#     -D PKG_MOLECULE=on -D PKG_KSPACE=on -D BUILD_SHARED_LIBS=on -D PKG_PYTHON=on -D FFT=KISS \
+#     -D CMAKE_INSTALL_PREFIX=`python3 -c "import sys; print(sys.prefix)"` -D Python_EXECUTABLE=`which python3`
+#
+# If the build succeeds, the shared library liblammps.so is installed into $CMAKE_INSTALL_PREFIX/lib64.
+# We also need the shared lib libpython3.x.so.1, which is under $CMAKE_INSTALL_PREFIX/lib.
+# Finally, libdlext.so installed by lammps.dlext is currently not found, so we need to add
+# $CMAKE_INSTALL_PREFIX/lib/python3.9/site-packages/lammps to LD_LIBRARY_PATH.
+#
+# export LD_LIBRARY_PATH=$CMAKE_INSTALL_PREFIX/lib64/lib:$CMAKE_INSTALL_PREFIX/lib64:$CMAKE_INSTALL_PREFIX/lib/python3.9/site-packages/lammps:$LD_LIBRARY_PATH
+#
+# where $CMAKE_INSTALL_PREFIX is the full path to the top-level folder of the virtual environment.
+#
+# To test the installation of the LAMMPS python module
+#      python3 -c "from lammps import lammps; lmp = lammps()"
+#
+
+from __future__ import print_function
+import sys
+
+import lammps
+from lammps import lammps
+
+def main():
+
+    # parse command line   
+    argv = sys.argv
+    if len(argv) != 2:
+      print("Syntax: ./simple.py in.lj")
+      sys.exit()
+
+    infile = sys.argv[1]
+
+    args = "-k on g 1 -sf kk"
+    #args += " -nocite -sc none"
+    args=args.split()
+    lmp = lammps(cmdargs=args)
+
+    # run infile one line at a time to set up the simulation
+    lines = open(infile,'r').readlines()
+    for line in lines: lmp.command(line)
+
+    # this is wrapped as the run method, see methods_dispatch run()
+    #   wrapped_context.run(timesteps, **kwargs) is called in methods/core.py
+    # do "run 0" to setup neighbor build and force computes
+    lmp.command("run 0")
+
+    # demo of how to extract simulation information from lmp (context)"
+    # see LMP_SRC/python/lammps/core.py, or under the installation path
+    #  $CMAKE_INSTALL_PREFIX/lib/python3.9/site-packages/lammps/core.py
+
+    print("----------------------------------------------")
+    print("Simulation info from the LAMMPS python module:")
+    natoms = lmp.extract_global("natoms")
+    print(f"natoms = {natoms}")
+    nlocal = lmp.extract_setting('nlocal')
+    print(f"nlocal = {nlocal}")
+
+    boxlo,boxhi,xy,yz,xz,periodicity,_ = lmp.extract_box()
+    print(f"box lo = {boxlo}")
+    print(f"box hi = {boxhi}")
+    Lx = boxhi[0] - boxlo[0]
+    Ly = boxhi[1] - boxlo[1]
+    Lz = boxhi[2] - boxlo[2]
+    origin = boxlo
+    H = ((Lx, xy * Ly, xz * Lz), (0.0, Ly, yz * Lz), (0.0, 0.0, Lz))
+    print("box matrix: ", H)
+
+    # or
+    #boxlo = lmp.extract_global("boxlo")
+    #boxhi = lmp.extract_global("boxhi")
+
+    dim = lmp.extract_setting('dimension')
+    print("Dimensionality = ", dim)
+    pe = lmp.get_thermo("pe")
+    print(f"Current potential energy = {pe}")
+
+    dt = lmp.extract_global("dt")
+    print(f"Timestep dt = {dt}")
+
+    # Query if PKG_KOKKOS is enabled
+    pkg_kokkos_enabled = lmp.has_package('KOKKOS')
+    print(f"KOKKOS enabled = {pkg_kokkos_enabled}")
+
+    on_gpu = False
+    kokkos_backends = {}
+    if pkg_kokkos_enabled == True:
+        kokkos_backends = lmp.accelerator_config["KOKKOS"]
+        if 'cuda' in kokkos_backends["api"]:
+          on_gpu = True
+    if on_gpu:
+      print('  - KOKKOS with CUDA backend')
+    else:
+      print(kokkos_backends["api"])
+
+    print("----------------------------------------------")
+
+    # this is necessary to shut down the MPI communication when Kokkos environment is active
+    lmp.finalize()
+
+if __name__ == "__main__":
+    main()