compatibility with new lammps-user-pace library and cleanup

examples/PACKAGES/pace/README.md

@@ -0,0 +1,9 @@
+# This folder contains examples for pace in LAMMPS
+
+
+## Compute pace usage
+compute/latte_cell_0.data            # lammps data file with C-H-O structure
+compute/latte_cell_0.xyz             # xyz file with C-H-O structure 
+compute/coupling_coefficients.yace   # .yace file containing coupling coefficients (or ACE potential parameters)
+compute/in.lammps                    # input file for calling `compute pace`
+

examples/PACKAGES/pace/compute/in.lammps

@@ -0,0 +1,22 @@
+#info all out log
+units  metal
+atom_style  atomic
+boundary    p p p
+atom_modify    map hash
+boundary  p p p
+read_data  latte_cell_0.data
+mass  1 1.00
+mass  2 14.00
+mass  3 15.999
+
+        # potential settings
+
+pair_style     zero 5.7
+pair_coeff     * *
+
+compute     pace all pace coupling_coefficients.yace 1 0
+
+thermo 1 
+thermo_style  custom step temp c_pace[1][183]
+
+run 0

examples/pace/multi-elem/README.md

@@ -1,5 +0,0 @@
-Check that seg fault doesn't occur by doing:
-
-    ./loop.sh
-
-which will loop through many runs of `python test_en.py`.

examples/pace/multi-elem/loop.sh

@@ -1,8 +0,0 @@
-for (( ; ; ))
-do 
-    python test_en.py
-    # terminate loop if seg fault
-    if [[ $? -eq 139 ]]; then 
-        break 
-    fi
-done

examples/pace/multi-elem/test_en.py

@@ -1,86 +0,0 @@
-from __future__ import print_function
-import sys, os
-import ctypes
-import numpy as np
-from ase.io import read,write
-from lammps import lammps, LMP_TYPE_ARRAY, LMP_STYLE_GLOBAL
-
-# get MPI settings from LAMMPS
-def run_struct(f):
-    file_prefix = f.split('.')[0]
-    atoms = read(f)
-    lmp = lammps()
-
-    me = lmp.extract_setting("world_rank")
-    nprocs = lmp.extract_setting("world_size")
-
-    write('%s.data' % file_prefix,atoms,format='lammps-data')
-
-    cmds = ["-screen", "none", "-log", "none"]
-    lmp = lammps(cmdargs = cmds)
-
-    print("Made LAMMPS instance")
-
-    def run_lammps(dgradflag):
-
-        # simulation settings
-        fname = file_prefix
-        lmp.command("clear")
-        lmp.command("info all out log")
-        lmp.command('units  metal')
-        lmp.command('atom_style  atomic')
-        lmp.command("boundary    p p p")
-        lmp.command("atom_modify    map hash")
-        lmp.command('neighbor  2.3 bin')
-        # boundary
-        lmp.command('boundary  p p p')
-        # read atoms
-        lmp.command('read_data  %s.data' % fname )
-        lmp.command('mass  1 1.00')
-        lmp.command('mass  2 14.00')
-        lmp.command('mass  3 15.999')
-
-        # potential settings
-
-        lmp.command(f"pair_style     zero 5.7")
-        lmp.command(f"pair_coeff     * *")
-
-
-        if dgradflag:
-            lmp.command(f"compute     pace all pace coupling_coefficients.yace 1 1")
-        else:
-            lmp.command(f"compute     pace all pace coupling_coefficients.yace 1 0 ")
-
-        # run
-
-        lmp.command(f"thermo         100")
-        lmp.command(f"run {nsteps}")
-
-    # declare simulation/structure variables
-
-    nsteps = 0
-    ntypes = 3
-
-    # declare compute pace variables
-
-
-    bikflag = 1
-
-    # NUMBER of descriptors
-    nd = 91
-
-    dgradflag = 0
-    
-    run_lammps(dgradflag)
-    
-    lmp_pace = lmp.numpy.extract_compute("pace", LMP_STYLE_GLOBAL, LMP_TYPE_ARRAY)
-    print ('global shape',np.shape(lmp_pace))
-    np.save('%s_chi_i.npy' % file_prefix,lmp_pace)
-    lmp.close()
-    del lmp
-    return None
-
-import glob
-for f in sorted(glob.glob('*.xyz')):
-    print ('running %s' % f)
-    run_struct(f)