import silicon testing framework

compress sparseX files to fit in GitHub size limits

README.md

@@ -1,2 +1,7 @@
 # silicon-testing-framework
 Testing framework for silicon interatomic potentials
+
+* `models` directory containing each model (DFTB and analytical interatomic potentials)
+* `tests` scripts for doing tests
+* `share` utilities used by tests
+* `test-runner` place to run tests, including script that actually runs a given test with a given model 

models/CASTEP_ASE/model.py

@@ -0,0 +1,52 @@
+import os
+from distutils import spawn
+
+#from matscipy.socketcalc import CastepClient, SocketCalculator
+from ase.calculators.castep import Castep
+
+model_abs_dir = os.path.abspath(os.path.dirname(__file__))
+
+if 'CASTEP_COMMAND' in os.environ:
+      castep = os.environ['CASTEP_COMMAND']
+else:
+      castep = spawn.find_executable('castep.serial')
+
+if 'MPIRUN' in os.environ:
+      mpirun = os.environ['MPIRUN']
+else:
+      mpirun = spawn.find_executable('mpirun')
+
+mpirun_args = ''
+if 'MPIRUN_ARGS' in os.environ:
+      mpirun_args = os.environ['MPIRUN_ARGS']
+
+os.environ['CASTEP_COMMAND'] = '{0} {1} {2}'.format(mpirun, mpirun_args, castep)
+
+name = 'CASTEP'
+Castep.name = name
+Castep.todict = lambda self: {}
+
+no_checkpoint = True
+
+def start(test_name):
+    global calculator
+    calculator = Castep(directory=test_name,
+                        cut_off_energy=250,
+                        spin_polarized=False,
+                        opt_strategy='speed',
+                        xc_functional='PW91',
+                        elec_energy_tol='0.0000001',
+                        max_scf_cycles=250,
+                        fix_occupancy=False,
+                        calculate_stress=True,
+                        finite_basis_corr='automatic',
+                        smearing_width='0.05',
+                        fine_grid_scale=4,
+                        mixing_scheme='pulay',
+                        mix_history_length=20,
+                        num_dump_cycles=0,
+                        kpoints_mp_spacing='0.030', # note that other values were used for some tests, e.g. 0.015 for bulk E(V), 0.07 for minimization of GAP amorphous structures, and perhaps some other variations
+                        species_pot = ("Si","{}/Si_OTF.usp".format(model_abs_dir)),
+                        perc_extra_bands=200)
+
+#                        symmetry_generate=False,

models/DFTB.1/model.py

@@ -0,0 +1,21 @@
+import os
+
+from quippy import Potential
+import __builtin__
+
+orig_dir = os.getcwd()
+model_dir = os.path.dirname(__file__)
+os.chdir(model_dir)
+try:
+    if hasattr(__builtin__, 'mpi_glob'):
+        calculator = Potential(init_args='TB DFTB use_k_density k_density=4.0 Fermi_T=0.05',
+                                               param_filename='tightbind.parms.DFTB.pbc-0-1.xml', mpi_obj=mpi_glob)
+    else:
+        calculator = Potential(init_args='TB DFTB use_k_density k_density=4.0 Fermi_T=0.05',
+                                               param_filename='tightbind.parms.DFTB.pbc-0-1.xml')
+finally:
+    os.chdir(orig_dir)
+
+no_checkpoint = True
+
+name = 'DFTB.1'

models/DFTB.1_fixed_kmesh/model.py

@@ -0,0 +1,21 @@
+import os
+
+from quippy import Potential
+import __builtin__
+
+orig_dir = os.getcwd()
+model_dir = os.path.dirname(__file__)
+os.chdir(model_dir)
+try:
+    if hasattr(__builtin__, 'mpi_glob'):
+        calculator = Potential(init_args='TB DFTB use_k_density_once k_density=4.0 Fermi_T=0.05',
+                                               param_filename='tightbind.parms.DFTB.pbc-0-1.xml', mpi_obj=mpi_glob)
+    else:
+        calculator = Potential(init_args='TB DFTB use_k_density_once k_density=4.0 Fermi_T=0.05',
+                                               param_filename='tightbind.parms.DFTB.pbc-0-1.xml')
+finally:
+    os.chdir(orig_dir)
+
+no_checkpoint = True
+
+name = 'DFTB.1'

models/DFTB.5/model.py

@@ -0,0 +1,21 @@
+import os
+
+from quippy import Potential
+import __builtin__
+
+orig_dir = os.getcwd()
+model_dir = os.path.dirname(__file__)
+os.chdir(model_dir)
+try:
+    if hasattr(__builtin__, 'mpi_glob'):
+        calculator = Potential(init_args='TB DFTB use_k_density k_density=20.0 Fermi_T=0.05',
+                                               param_filename='tightbind.parms.DFTB.pbc-0-1.xml', mpi_obj=mpi_glob)
+    else:
+        calculator = Potential(init_args='TB DFTB use_k_density k_density=20.0 Fermi_T=0.05',
+                                               param_filename='tightbind.parms.DFTB.pbc-0-1.xml')
+finally:
+    os.chdir(orig_dir)
+
+no_checkpoint = True
+
+name = 'DFTB.5'

models/EDIP/Si.edip

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+# DATE: 2011-09-15 CONTRIBUTOR: Unknown CITATION: Justo, Bazant, Kaxiras, Bulatov and Yip, Phys Rev B, 58, 2539 (1998)
+
+# EDIP parameters for various elements and mixtures
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# these entries are in LAMMPS "metal" units
+
+# format of a single entry (one or more lines)
+#
+#   element 1, element 2, element 3, 
+#     A   B   cutoffA   cutoffC   alpha   beta   eta 
+#     gamma   lambda    mu   rho   sigma   Q0 
+#     u1   u2   u3   u4
+#
+# units for each parameters:
+#     A , lambda are in eV  
+#     B, cutoffA, cutoffC, gamma, sigma are in Angstrom
+#     alpha, beta, eta, mu, rho, Q0, u1-u4 are pure numbers 
+
+# Here are the original parameters in metal units, for Silicon from:
+# J. F. Justo, M. Z. Bazant, E. Kaxiras, V. V. Bulatov, S. Yip
+#       Phys. Rev. B 58, 2539 (1998)
+#
+
+Si Si Si 7.9821730 1.5075463 3.1213820 2.5609104 3.1083847 0.0070975 0.2523244
+         1.1247945 1.4533108 0.6966326 1.2085196 0.5774108 312.1341346
+         -0.165799 32.557 0.286198 0.66