From ddeb0cd31d8bbb46da400ea267e90752c7196c8f Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Thu, 22 Mar 2018 18:51:58 -0400
Subject: [PATCH] Tools: draft basic SQLite functionality for Python driver.
---
tools/driver.py | 197 ++++++++++++++++++++++++++++++++++++++++++++++--
1 file changed, 191 insertions(+), 6 deletions(-)
diff --git a/tools/driver.py b/tools/driver.py
index 59a8c4a8..93163dea 100644
--- a/tools/driver.py
+++ b/tools/driver.py
@@ -1,6 +1,9 @@
#!/bin/python3
-from ctypes import *
+from ctypes import c_int, c_double, c_char, c_char_p, c_void_p, \
+ Structure, Union, POINTER, CFUNCTYPE, cdll
+import sqlite3 as sq3
+from os import path
class BondOrderData(Structure):
@@ -220,7 +223,6 @@ class SimulationData(Structure):
("ext_press", c_double * 3),
("kin_press", c_double),
("tot_press", c_double * 3),
- ("tot_press", c_double * 3),
("timing", ReaxTiming),
]
@@ -236,6 +238,141 @@ class ReaxAtom(Structure):
]
+def create_db(name='spuremd.db'):
+ conn = sq3.connect(name)
+
+ conn.executescript("""
+ CREATE TABLE simulation(
+ id integer,
+ date text,
+ name text,
+ ensemble_type integer,
+ steps integer,
+ time_step integer,
+ restart_format integer,
+ random_velocity integer,
+ reposition_atoms integer,
+ peroidic_boundary integer,
+ geo_format integer,
+ restrict_bonds integer,
+ tabulate_long_range integer,
+ reneighbor integer,
+ vlist_cutoff real,
+ neighbor_cutoff real,
+ three_body_cutoff real,
+ hydrogen_bond_cutoff real,
+ bond_graph_cutoff real,
+ charge_method integer,
+ cm_q_net real,
+ cm_solver_type integer,
+ cm_solver_max_iters integer,
+ cm_solver_restart integer,
+ cm_solver_q_err real,
+ cm_domain_sparsity real,
+ cm_solver_pre_comp_type integer,
+ cm_solver_pre_comp_refactor integer,
+ cm_solver_pre_comp_droptol real,
+ cm_solver_pre_comp_sweeps integer,
+ cm_solver_pre_comp_sai_thres real,
+ cm_solver_pre_app_type integer,
+ cm_solver_pre_app_jacobi_iters integer,
+ temp_init real,
+ temp_final real,
+ temp_mass real,
+ temp_mode integer,
+ temp_rate real,
+ temp_freq integer,
+ pressure real,
+ pressure_mass real,
+ compress integer,
+ pressure_mode integer,
+ remove_center_of_mass integer,
+ debug_level integer,
+ write_freq integer,
+ traj_compress integer,
+ traj_format integer,
+ traj_title text,
+ atom_info integer,
+ atom_velocities integer,
+ atom_forces integer,
+ bond_info integer,
+ angle_info integer,
+ test_forces integer,
+ molecule_analysis integer,
+ freq_molecule_analysis integer,
+ ignore integer,
+ dipole_analysis integer,
+ freq_dipole_analysis integer,
+ diffusion_coefficient integer,
+ freq_diffusion_coefficient integer,
+ restrict_type integer,
+ PRIMARY KEY (id)
+ );
+
+ CREATE TABLE system_properties(
+ id integer,
+ step integer,
+ total_energy real,
+ potential_energy real,
+ kinetic_energy real,
+ temperature real,
+ volume real,
+ pressure real,
+ PRIMARY KEY (id, step)
+ );
+
+ CREATE TABLE potential(
+ id integer,
+ step integer,
+ bond_energy real,
+ atom_energy real,
+ lone_pair_energy real,
+ angle_energy real,
+ coa_energy real,
+ hydrogen_bond_energy real,
+ torsion_energy real,
+ conjugation_energy real,
+ van_der_waals_energy real,
+ coulombic_energy real,
+ polarization_energy real,
+ PRIMARY KEY (id, step)
+ );
+
+ CREATE TABLE trajectory(
+ id integer,
+ step integer,
+ atom_id integer,
+ position_x real,
+ position_y real,
+ position_z real,
+ charge real,
+ PRIMARY KEY (id, step, atom_id)
+ );
+
+ CREATE TABLE performance(
+ id integer,
+ step integer,
+ time_total real,
+ time_nbrs real,
+ time_init real,
+ time_bonded real,
+ time_nonbonded real,
+ time_cm real,
+ time_cm_sort real,
+ cm_solver_iters integer,
+ time_cm_pre_comp real,
+ time_cm_pre_app real,
+ time_cm_solver_spmv real,
+ time_cm_solver_vec_ops real,
+ time_cm_solver_orthog real,
+ time_cm_solver_tri_solve real,
+ PRIMARY KEY (id, step)
+ );
+ """)
+
+ conn.close()
+
+
if __name__ == '__main__':
lib = cdll.LoadLibrary("libspuremd.so.1")
@@ -258,10 +395,6 @@ if __name__ == '__main__':
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
@@ -269,6 +402,57 @@ if __name__ == '__main__':
set_output_enabled.argtypes = [c_void_p, c_int]
set_output_enabled.restype = c_int
+ db_file = "spuremd.db"
+
+ if not path.isfile(db_file):
+ create_db(db_file)
+
+ conn = sq3.connect(db_file)
+ record_potential = True
+ record_trajectory = False
+ record_performance = True
+
+ 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))
+
+ if data[0].step == 0:
+ #TODO: insert data into simulation table
+ pass
+
+ with conn:
+ conn.execute("INSERT INTO system_properties VALUES (?,?,?,?,?,?,?,?)",
+ (0, data[0].step, data[0].E_Tot, data[0].E_Pot, data[0].E_Kin,
+ data[0].therm.T, 0.0, data[0].iso_bar.P))
+ # MISSING: ID, system->box.volume
+
+ if record_potential:
+ with conn:
+ conn.execute("INSERT INTO potential VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?)",
+ (0, data[0].step, data[0].E_BE, data[0].E_Ov + data[0].E_Un,
+ data[0].E_Lp, data[0].E_Ang + data[0].E_Pen, data[0].E_Coa,
+ data[0].E_HB, data[0].E_Tor, data[0].E_Con, data[0].E_vdW,
+ data[0].E_Ele, data[0].E_Pol))
+
+ if record_trajectory:
+ with conn:
+ for i in range(6540):
+ conn.execute("INSERT INTO trajectory VALUES (?,?,?,?,?,?,?)",
+ (0, data[0].step, i, atoms[i].x[0], atoms[i].x[1],
+ atoms[i].x[2], atoms[i].q))
+
+ if record_performance:
+ with conn:
+ conn.execute("INSERT INTO performance VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)",
+ (0, data[0].step, data[0].timing.total, data[0].timing.nbrs, data[0].timing.init_forces,
+ data[0].timing.bonded, data[0].timing.nonb, data[0].timing.cm,
+ data[0].timing.cm_sort_mat_rows, data[0].timing.cm_solver_iters,
+ data[0].timing.cm_solver_pre_comp,
+ data[0].timing.cm_solver_pre_app, data[0].timing.cm_solver_spmv,
+ data[0].timing.cm_solver_vector_ops, data[0].timing.cm_solver_orthog,
+ data[0].timing.cm_solver_tri_solve))
+
+
handle = setup(b"data/benchmarks/water/water_6540.pdb",
b"data/benchmarks/water/ffield.water",
b"environ/param.gpu.water")
@@ -288,4 +472,5 @@ if __name__ == '__main__':
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))
+ conn.close()
cleanup(handle)
--
GitLab