diff --git a/tools/driver.py b/tools/driver.py
index 0144e62cb45ad5b107deb565d6c5b1877a32725f..12a4a0882981ef73d8b252dbb360505e830d35f4 100644
--- a/tools/driver.py
+++ b/tools/driver.py
@@ -3,6 +3,123 @@
from ctypes import *
+class BondOrderData(Structure):
+ _fields_ = [
+ ("BO", c_double),
+ ("BO_s", c_double),
+ ("BO_pi", c_double),
+ ("BO_pi2", c_double),
+ ("Cdbo", c_double),
+ ("Cdbopi", c_double),
+ ("Cdbopi2", c_double),
+ ("C1dbo", c_double),
+ ("C2dbo", c_double),
+ ("C3dbo", c_double),
+ ("C1dbopi", c_double),
+ ("C2dbopi", c_double),
+ ("C3dbopi", c_double),
+ ("C4dbopi", c_double),
+ ("C1dbopi2", c_double),
+ ("C2dbopi2", c_double),
+ ("C3dbopi2", c_double),
+ ("C4dbopi2", c_double),
+ ("dBOp", c_double * 3),
+ ("dln_BOp_s", c_double * 3),
+ ("dln_BOp_pi", c_double * 3),
+ ("dln_BOp_pi2", c_double * 3),
+ ]
+
+
+class ThreeBodyData(Structure):
+ _fields_ = [
+ ("thb", c_int),
+ ("pthb", c_int),
+ ("theta", c_double),
+ ("cos_theta", c_double),
+ ("dcos_di", c_double * 3),
+ ("dcos_dj", c_double * 3),
+ ("dcos_dk", c_double * 3),
+ ]
+
+
+class BondData(Structure):
+ _fields_ = [
+ ("nbr", c_int),
+ ("sym_index", c_int),
+ ("dbond_index", c_int),
+ ("rel_box", c_int * 3),
+ ("d", c_double),
+ ("dvec", c_double * 3),
+ ("bo_data", BondOrderData),
+ ]
+
+
+class DBondData(Structure):
+ _fields_ = [
+ ("wrt", c_int),
+ ("dBO", c_double * 3),
+ ("dBOpi", c_double * 3),
+ ("dBOpi2", c_double * 3),
+ ]
+
+
+class DDeltaData(Structure):
+ _fields_ = [
+ ("wrt", c_int),
+ ("dVal", c_double * 3),
+ ]
+
+
+class FarNbrData(Structure):
+ _fields_ = [
+ ("nbr", c_int),
+ ("rel_box", c_int * 3),
+ ("d", c_double),
+ ("dvec", c_double * 3),
+ ]
+
+
+class NearNbrData(Structure):
+ _fields_ = [
+ ("nbr", c_int),
+ ("rel_box", c_int * 3),
+ ("d", c_double),
+ ("dvec", c_double * 3),
+ ]
+
+
+class HBondData(Structure):
+ _fields_ = [
+ ("nbr", c_int),
+ ("scl", c_int),
+ ("ptr", POINTER(FarNbrData)),
+ ]
+
+
+class ReaxListSelector(Union):
+ _fields_ = [
+ ("v", c_void_p),
+ ("three_body_interaction_data", POINTER(ThreeBodyData)),
+ ("bond_data", POINTER(BondData)),
+ ("dbond_data", POINTER(DBondData)),
+ ("dDelta_data", POINTER(DDeltaData)),
+ ("far_neighbor_data", POINTER(FarNbrData)),
+ ("near_neighbor_data", POINTER(NearNbrData)),
+ ("hbond_data", POINTER(HBondData)),
+ ]
+
+
+class ReaxList(Structure):
+ _fields_ = [
+ ("n", c_int),
+ ("total_intrs", c_int),
+ ("index", POINTER(c_int)),
+ ("end_index", POINTER(c_int)),
+ ("max_intrs", POINTER(c_int)),
+ ("select", ReaxListSelector),
+ ]
+
+
class Thermostat(Structure):
_fields_ = [
("T", c_double),
@@ -133,10 +250,35 @@ if __name__ == '__main__':
cleanup.argtypes = [c_void_p]
cleanup.restype = c_int
+ get_atoms = lib.get_atoms
+ get_atoms.argtypes = [c_void_p]
+ get_atoms.restype = POINTER(ReaxAtom)
+
+ CALLBACKFUNC = CFUNCTYPE(None, POINTER(ReaxAtom),
+ POINTER(SimulationData), POINTER(ReaxList))
+
+ def get_simulation_step_results(atoms, data, lists):
+ print("{0:24.15f} {1:24.15f} {2:24.15f}".format(
+ data[0].E_Tot, data[0].E_Kin, data[0].E_Pot))
+
+ setup_callback = lib.setup_callback
+ setup_callback.restype = c_int
+
handle = setup(b"data/benchmarks/water/water_6540.pdb",
b"data/benchmarks/water/ffield.water",
b"environ/param.gpu.water")
- simulate(handle)
+ ret = setup_callback(handle, CALLBACKFUNC(get_simulation_step_results))
+
+ print("{0:24}|{1:24}|{2:24}".format("Total Energy", "Kinetic Energy", "Potential Energy"))
+ ret = simulate(handle)
+
+ atoms = get_atoms(handle)
+
+ print()
+ print("{0:9}|{1:24}|{2:24}|{3:24}|{4:24}".format("Atom Num", "x-Position", "y-Position", "z-Position", "Charge"))
+ for i in range(10):
+ print("{0:9d} {1:24.15f} {2:24.15f} {3:24.15f} {4:24.15f}".format(
+ i + 1, atoms[i].x[0], atoms[i].x[1], atoms[i].x[2], atoms[i].q))
cleanup(handle)
diff --git a/tools/run_sim.py b/tools/run_sim.py
index e8c56f0d61a59f327651cbb96a968e56746eda3f..3f3af62e8840486ef17a47a5000f9819a0bcb9b1 100644
--- a/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -79,9 +79,11 @@ class TestCase():
fp_temp.write(lines)
fp_temp.close()
- def run(self, bin_file='sPuReMD/bin/spuremd', process_results=False):
- base_dir = getcwd()
- bin_path = path.join(base_dir, bin_file)
+ def run(self, binary, process_results=False):
+ args = binary.split()
+ args.append(self.__geo_file)
+ args.append( self.__ffield_file)
+ args.append("")
env = dict(environ)
write_header = True
@@ -111,14 +113,13 @@ class TestCase():
+ '_paji' + param_dict['cm_solver_pre_app_jacobi_iters'] \
+ '_t' + param_dict['threads']
-
if not process_results:
self._setup(param_dict, temp_file)
env['OMP_NUM_THREADS'] = param_dict['threads']
start = time()
- proc_handle = Popen([bin_path, self.__geo_file, self.__ffield_file, temp_file],
- stdout=PIPE, stderr=PIPE, env=env, universal_newlines=True)
+ args[-1] = temp_file
+ proc_handle = Popen(args, stdout=PIPE, stderr=PIPE, env=env, universal_newlines=True)
stdout, stderr = proc_handle.communicate()
stop = time()
if proc_handle.returncode < 0:
@@ -202,6 +203,8 @@ if __name__ == '__main__':
]
parser = argparse.ArgumentParser(description='Run molecular dynamics simulations on specified data sets.')
+ parser.add_argument('-b', '--binary', metavar='binary', default=None, nargs=1,
+ help='Binary file to run.')
parser.add_argument('-f', '--out_file', metavar='out_file', default=None, nargs=1,
help='Output file to write results.')
parser.add_argument('-r', '--process_results', default=False, action='store_true',
@@ -250,6 +253,11 @@ if __name__ == '__main__':
else:
result_file = 'result.txt'
+ if args.binary:
+ binary = args.binary[0]
+ else:
+ binary = path.join(base_dir, 'sPuReMD/bin/spuremd')
+
# overwrite default params, if supplied via command line args
if args.params:
for param in args.params:
@@ -342,4 +350,4 @@ if __name__ == '__main__':
geo_format=['1'], result_file=result_file))
for test in test_cases:
- test.run(bin_file='sPuReMD/bin/spuremd', process_results=args.process_results)
+ test.run(binary, process_results=args.process_results)