From fd3d22592e82e3c2565b424e0de6029675d94719 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Mon, 22 Oct 2018 12:35:44 -0400
Subject: [PATCH] Tools: update run_sim.py to work with absolute paths (by
refereing supplied executable path). Begin updating testing scripts.
---
test_harness/control_bilayer_340800_serial | 68 --------
test_harness/control_bilayer_56800_serial | 68 --------
test_harness/control_silica_300000_serial | 68 --------
test_harness/control_silica_6000_serial | 68 --------
test_harness/control_silica_72000_serial | 68 --------
test_harness/control_water_327000_serial | 68 --------
test_harness/control_water_6540_serial | 68 --------
test_harness/control_water_78480_serial | 68 --------
test_harness/submit_short_jobs.bash | 173 +++++++++++---------
tools/run_sim.py | 177 +++++++++++++++------
10 files changed, 225 insertions(+), 669 deletions(-)
delete mode 100644 test_harness/control_bilayer_340800_serial
delete mode 100644 test_harness/control_bilayer_56800_serial
delete mode 100644 test_harness/control_silica_300000_serial
delete mode 100644 test_harness/control_silica_6000_serial
delete mode 100644 test_harness/control_silica_72000_serial
delete mode 100644 test_harness/control_water_327000_serial
delete mode 100644 test_harness/control_water_6540_serial
delete mode 100644 test_harness/control_water_78480_serial
diff --git a/test_harness/control_bilayer_340800_serial b/test_harness/control_bilayer_340800_serial
deleted file mode 100644
index 7087989c..00000000
--- a/test_harness/control_bilayer_340800_serial
+++ /dev/null
@@ -1,68 +0,0 @@
-simulation_name bilayer_340800_notab_nve_qeq_serial ! output files will carry this name + their specific extension
-ensemble_type 0 ! 0: NVE, 1: Berendsen NVT, 2: nose-Hoover NVT, 3: semi-isotropic NPT, 4: isotropic NPT, 5: anisotropic NPT
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
-
-reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
-restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
-tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
-remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
-
-nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
-thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
-
-charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
-cm_q_net 0.0 ! net system charge
-cm_solver_type 0 ! iterative linear solver for charge method: 0 = GMRES(k), 1 = GMRES_H(k), 2 = CG, 3 = SDM
-cm_solver_max_iters 20 ! max solver iterations
-cm_solver_restart 100 ! inner iterations of before restarting (GMRES(k)/GMRES_H(k))
-cm_solver_q_err 1e-6 ! relative residual norm threshold used in solver
-cm_domain_sparsity 1.0 ! scalar for scaling cut-off distance, used to sparsify charge matrix (between 0.0 and 1.0)
-cm_init_guess_extrap1 3 ! order of spline extrapolation for initial guess (s)
-cm_init_guess_extrap2 2 ! order of spline extrapolation for initial guess (t)
-cm_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
-cm_solver_pre_comp_refactor 1000 ! number of steps before recomputing preconditioner
-cm_solver_pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (FG-ILUT)
-cm_solver_pre_comp_sai_thres 0.1 ! ratio of charge matrix NNZ's used to compute preconditioner (SAI)
-cm_solver_pre_app_type 1 ! method used to apply preconditioner (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_app_jacobi_iters 50 ! num. Jacobi iterations used for applying precondition (ICHOLT/ILUT/FG-ILUT)
-
-temp_init 0.0 ! desired initial temperature of the simulated system
-temp_final 300.0 ! desired final temperature of the simulated system
-t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
-t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
-t_rate -100.0 ! in K
-t_freq 4.0 ! in ps
-
-pressure 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 5000.00 ! in fs, pressure inertia parameter
-compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
-press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
-
-geo_format 0 ! 0: custom, 1: pdb, 2: bgf
-write_freq 0 ! write trajectory after so many steps
-traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
-traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
-traj_title WATER_NVE ! (no white spaces)
-atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
-atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
-atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
-bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
-angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
-test_forces 0 ! 0: normal run, 1: at every timestep print each force type into a different file
-
-molec_anal 0 ! 1: outputs newly formed molecules as the simulation progresses
-freq_molec_anal 0 ! perform molecular analysis at every 'this many' timesteps
-dipole_anal 0 ! 1: calculate a electric dipole moment of the system
-freq_dipole_anal 1 ! calculate electric dipole moment at every 'this many' steps
-diffusion_coef 0 ! 1: calculate diffusion coefficient of the system
-freq_diffusion_coef 1 ! calculate diffusion coefficient at every 'this many' steps
-restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
diff --git a/test_harness/control_bilayer_56800_serial b/test_harness/control_bilayer_56800_serial
deleted file mode 100644
index a3cc7de0..00000000
--- a/test_harness/control_bilayer_56800_serial
+++ /dev/null
@@ -1,68 +0,0 @@
-simulation_name bilayer_56800_notab_nve_qeq_serial ! output files will carry this name + their specific extension
-ensemble_type 0 ! 0: NVE, 1: Berendsen NVT, 2: nose-Hoover NVT, 3: semi-isotropic NPT, 4: isotropic NPT, 5: anisotropic NPT
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
-
-reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
-restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
-tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
-remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
-
-nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
-thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
-
-charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
-cm_q_net 0.0 ! net system charge
-cm_solver_type 0 ! iterative linear solver for charge method: 0 = GMRES(k), 1 = GMRES_H(k), 2 = CG, 3 = SDM
-cm_solver_max_iters 20 ! max solver iterations
-cm_solver_restart 100 ! inner iterations of before restarting (GMRES(k)/GMRES_H(k))
-cm_solver_q_err 1e-6 ! relative residual norm threshold used in solver
-cm_domain_sparsity 1.0 ! scalar for scaling cut-off distance, used to sparsify charge matrix (between 0.0 and 1.0)
-cm_init_guess_extrap1 3 ! order of spline extrapolation for initial guess (s)
-cm_init_guess_extrap2 2 ! order of spline extrapolation for initial guess (t)
-cm_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
-cm_solver_pre_comp_refactor 1000 ! number of steps before recomputing preconditioner
-cm_solver_pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (FG-ILUT)
-cm_solver_pre_comp_sai_thres 0.1 ! ratio of charge matrix NNZ's used to compute preconditioner (SAI)
-cm_solver_pre_app_type 1 ! method used to apply preconditioner (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_app_jacobi_iters 50 ! num. Jacobi iterations used for applying precondition (ICHOLT/ILUT/FG-ILUT)
-
-temp_init 0.0 ! desired initial temperature of the simulated system
-temp_final 300.0 ! desired final temperature of the simulated system
-t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
-t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
-t_rate -100.0 ! in K
-t_freq 4.0 ! in ps
-
-pressure 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 5000.00 ! in fs, pressure inertia parameter
-compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
-press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
-
-geo_format 1 ! 0: custom, 1: pdb, 2: bgf
-write_freq 0 ! write trajectory after so many steps
-traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
-traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
-traj_title WATER_NVE ! (no white spaces)
-atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
-atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
-atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
-bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
-angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
-test_forces 0 ! 0: normal run, 1: at every timestep print each force type into a different file
-
-molec_anal 0 ! 1: outputs newly formed molecules as the simulation progresses
-freq_molec_anal 0 ! perform molecular analysis at every 'this many' timesteps
-dipole_anal 0 ! 1: calculate a electric dipole moment of the system
-freq_dipole_anal 1 ! calculate electric dipole moment at every 'this many' steps
-diffusion_coef 0 ! 1: calculate diffusion coefficient of the system
-freq_diffusion_coef 1 ! calculate diffusion coefficient at every 'this many' steps
-restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
diff --git a/test_harness/control_silica_300000_serial b/test_harness/control_silica_300000_serial
deleted file mode 100644
index 6fc327fe..00000000
--- a/test_harness/control_silica_300000_serial
+++ /dev/null
@@ -1,68 +0,0 @@
-simulation_name silica_300000_notab_nve_qeq_serial ! output files will carry this name + their specific extension
-ensemble_type 0 ! 0: NVE, 1: Berendsen NVT, 2: nose-Hoover NVT, 3: semi-isotropic NPT, 4: isotropic NPT, 5: anisotropic NPT
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
-
-reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
-restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
-tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
-remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
-
-nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
-thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
-
-charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
-cm_q_net 0.0 ! net system charge
-cm_solver_type 0 ! iterative linear solver for charge method: 0 = GMRES(k), 1 = GMRES_H(k), 2 = CG, 3 = SDM
-cm_solver_max_iters 20 ! max solver iterations
-cm_solver_restart 100 ! inner iterations of before restarting (GMRES(k)/GMRES_H(k))
-cm_solver_q_err 1e-6 ! relative residual norm threshold used in solver
-cm_domain_sparsity 1.0 ! scalar for scaling cut-off distance, used to sparsify charge matrix (between 0.0 and 1.0)
-cm_init_guess_extrap1 3 ! order of spline extrapolation for initial guess (s)
-cm_init_guess_extrap2 2 ! order of spline extrapolation for initial guess (t)
-cm_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
-cm_solver_pre_comp_refactor 1000 ! number of steps before recomputing preconditioner
-cm_solver_pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (FG-ILUT)
-cm_solver_pre_comp_sai_thres 0.1 ! ratio of charge matrix NNZ's used to compute preconditioner (SAI)
-cm_solver_pre_app_type 1 ! method used to apply preconditioner (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_app_jacobi_iters 50 ! num. Jacobi iterations used for applying precondition (ICHOLT/ILUT/FG-ILUT)
-
-temp_init 0.0 ! desired initial temperature of the simulated system
-temp_final 300.0 ! desired final temperature of the simulated system
-t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
-t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
-t_rate -100.0 ! in K
-t_freq 4.0 ! in ps
-
-pressure 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 5000.00 ! in fs, pressure inertia parameter
-compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
-press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
-
-geo_format 0 ! 0: custom, 1: pdb, 2: bgf
-write_freq 0 ! write trajectory after so many steps
-traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
-traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
-traj_title WATER_NVE ! (no white spaces)
-atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
-atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
-atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
-bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
-angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
-test_forces 0 ! 0: normal run, 1: at every timestep print each force type into a different file
-
-molec_anal 0 ! 1: outputs newly formed molecules as the simulation progresses
-freq_molec_anal 0 ! perform molecular analysis at every 'this many' timesteps
-dipole_anal 0 ! 1: calculate a electric dipole moment of the system
-freq_dipole_anal 1 ! calculate electric dipole moment at every 'this many' steps
-diffusion_coef 0 ! 1: calculate diffusion coefficient of the system
-freq_diffusion_coef 1 ! calculate diffusion coefficient at every 'this many' steps
-restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
diff --git a/test_harness/control_silica_6000_serial b/test_harness/control_silica_6000_serial
deleted file mode 100644
index 5b4cee39..00000000
--- a/test_harness/control_silica_6000_serial
+++ /dev/null
@@ -1,68 +0,0 @@
-simulation_name silica_6000_notab_nve_qeq_serial ! output files will carry this name + their specific extension
-ensemble_type 0 ! 0: NVE, 1: Berendsen NVT, 2: nose-Hoover NVT, 3: semi-isotropic NPT, 4: isotropic NPT, 5: anisotropic NPT
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
-
-reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
-restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
-tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
-remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
-
-nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
-thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
-
-charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
-cm_q_net 0.0 ! net system charge
-cm_solver_type 0 ! iterative linear solver for charge method: 0 = GMRES(k), 1 = GMRES_H(k), 2 = CG, 3 = SDM
-cm_solver_max_iters 20 ! max solver iterations
-cm_solver_restart 100 ! inner iterations of before restarting (GMRES(k)/GMRES_H(k))
-cm_solver_q_err 1e-6 ! relative residual norm threshold used in solver
-cm_domain_sparsity 1.0 ! scalar for scaling cut-off distance, used to sparsify charge matrix (between 0.0 and 1.0)
-cm_init_guess_extrap1 3 ! order of spline extrapolation for initial guess (s)
-cm_init_guess_extrap2 2 ! order of spline extrapolation for initial guess (t)
-cm_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
-cm_solver_pre_comp_refactor 1000 ! number of steps before recomputing preconditioner
-cm_solver_pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (FG-ILUT)
-cm_solver_pre_comp_sai_thres 0.1 ! ratio of charge matrix NNZ's used to compute preconditioner (SAI)
-cm_solver_pre_app_type 1 ! method used to apply preconditioner (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_app_jacobi_iters 50 ! num. Jacobi iterations used for applying precondition (ICHOLT/ILUT/FG-ILUT)
-
-temp_init 0.0 ! desired initial temperature of the simulated system
-temp_final 300.0 ! desired final temperature of the simulated system
-t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
-t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
-t_rate -100.0 ! in K
-t_freq 4.0 ! in ps
-
-pressure 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 5000.00 ! in fs, pressure inertia parameter
-compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
-press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
-
-geo_format 1 ! 0: custom, 1: pdb, 2: bgf
-write_freq 0 ! write trajectory after so many steps
-traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
-traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
-traj_title WATER_NVE ! (no white spaces)
-atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
-atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
-atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
-bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
-angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
-test_forces 0 ! 0: normal run, 1: at every timestep print each force type into a different file
-
-molec_anal 0 ! 1: outputs newly formed molecules as the simulation progresses
-freq_molec_anal 0 ! perform molecular analysis at every 'this many' timesteps
-dipole_anal 0 ! 1: calculate a electric dipole moment of the system
-freq_dipole_anal 1 ! calculate electric dipole moment at every 'this many' steps
-diffusion_coef 0 ! 1: calculate diffusion coefficient of the system
-freq_diffusion_coef 1 ! calculate diffusion coefficient at every 'this many' steps
-restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
diff --git a/test_harness/control_silica_72000_serial b/test_harness/control_silica_72000_serial
deleted file mode 100644
index 1990d37a..00000000
--- a/test_harness/control_silica_72000_serial
+++ /dev/null
@@ -1,68 +0,0 @@
-simulation_name silica_72000_notab_nve_qeq_serial ! output files will carry this name + their specific extension
-ensemble_type 0 ! 0: NVE, 1: Berendsen NVT, 2: nose-Hoover NVT, 3: semi-isotropic NPT, 4: isotropic NPT, 5: anisotropic NPT
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
-
-reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
-restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
-tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
-remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
-
-nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
-thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
-
-charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
-cm_q_net 0.0 ! net system charge
-cm_solver_type 0 ! iterative linear solver for charge method: 0 = GMRES(k), 1 = GMRES_H(k), 2 = CG, 3 = SDM
-cm_solver_max_iters 20 ! max solver iterations
-cm_solver_restart 100 ! inner iterations of before restarting (GMRES(k)/GMRES_H(k))
-cm_solver_q_err 1e-6 ! relative residual norm threshold used in solver
-cm_domain_sparsity 1.0 ! scalar for scaling cut-off distance, used to sparsify charge matrix (between 0.0 and 1.0)
-cm_init_guess_extrap1 3 ! order of spline extrapolation for initial guess (s)
-cm_init_guess_extrap2 2 ! order of spline extrapolation for initial guess (t)
-cm_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
-cm_solver_pre_comp_refactor 1000 ! number of steps before recomputing preconditioner
-cm_solver_pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (FG-ILUT)
-cm_solver_pre_comp_sai_thres 0.1 ! ratio of charge matrix NNZ's used to compute preconditioner (SAI)
-cm_solver_pre_app_type 1 ! method used to apply preconditioner (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_app_jacobi_iters 50 ! num. Jacobi iterations used for applying precondition (ICHOLT/ILUT/FG-ILUT)
-
-temp_init 0.0 ! desired initial temperature of the simulated system
-temp_final 300.0 ! desired final temperature of the simulated system
-t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
-t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
-t_rate -100.0 ! in K
-t_freq 4.0 ! in ps
-
-pressure 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 5000.00 ! in fs, pressure inertia parameter
-compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
-press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
-
-geo_format 0 ! 0: custom, 1: pdb, 2: bgf
-write_freq 0 ! write trajectory after so many steps
-traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
-traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
-traj_title WATER_NVE ! (no white spaces)
-atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
-atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
-atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
-bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
-angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
-test_forces 0 ! 0: normal run, 1: at every timestep print each force type into a different file
-
-molec_anal 0 ! 1: outputs newly formed molecules as the simulation progresses
-freq_molec_anal 0 ! perform molecular analysis at every 'this many' timesteps
-dipole_anal 0 ! 1: calculate a electric dipole moment of the system
-freq_dipole_anal 1 ! calculate electric dipole moment at every 'this many' steps
-diffusion_coef 0 ! 1: calculate diffusion coefficient of the system
-freq_diffusion_coef 1 ! calculate diffusion coefficient at every 'this many' steps
-restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
diff --git a/test_harness/control_water_327000_serial b/test_harness/control_water_327000_serial
deleted file mode 100644
index e895ac17..00000000
--- a/test_harness/control_water_327000_serial
+++ /dev/null
@@ -1,68 +0,0 @@
-simulation_name water_327000_notab_nve_qeq_serial ! output files will carry this name + their specific extension
-ensemble_type 0 ! 0: NVE, 1: Berendsen NVT, 2: nose-Hoover NVT, 3: semi-isotropic NPT, 4: isotropic NPT, 5: anisotropic NPT
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
-
-reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
-restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
-tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
-remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
-
-nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
-thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
-
-charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
-cm_q_net 0.0 ! net system charge
-cm_solver_type 0 ! iterative linear solver for charge method: 0 = GMRES(k), 1 = GMRES_H(k), 2 = CG, 3 = SDM
-cm_solver_max_iters 20 ! max solver iterations
-cm_solver_restart 100 ! inner iterations of before restarting (GMRES(k)/GMRES_H(k))
-cm_solver_q_err 1e-6 ! relative residual norm threshold used in solver
-cm_domain_sparsity 1.0 ! scalar for scaling cut-off distance, used to sparsify charge matrix (between 0.0 and 1.0)
-cm_init_guess_extrap1 3 ! order of spline extrapolation for initial guess (s)
-cm_init_guess_extrap2 2 ! order of spline extrapolation for initial guess (t)
-cm_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
-cm_solver_pre_comp_refactor 1000 ! number of steps before recomputing preconditioner
-cm_solver_pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (FG-ILUT)
-cm_solver_pre_comp_sai_thres 0.1 ! ratio of charge matrix NNZ's used to compute preconditioner (SAI)
-cm_solver_pre_app_type 1 ! method used to apply preconditioner (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_app_jacobi_iters 50 ! num. Jacobi iterations used for applying precondition (ICHOLT/ILUT/FG-ILUT)
-
-temp_init 0.0 ! desired initial temperature of the simulated system
-temp_final 300.0 ! desired final temperature of the simulated system
-t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
-t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
-t_rate -100.0 ! in K
-t_freq 4.0 ! in ps
-
-pressure 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 5000.00 ! in fs, pressure inertia parameter
-compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
-press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
-
-geo_format 0 ! 0: custom, 1: pdb, 2: bgf
-write_freq 0 ! write trajectory after so many steps
-traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
-traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
-traj_title WATER_NVE ! (no white spaces)
-atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
-atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
-atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
-bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
-angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
-test_forces 0 ! 0: normal run, 1: at every timestep print each force type into a different file
-
-molec_anal 0 ! 1: outputs newly formed molecules as the simulation progresses
-freq_molec_anal 0 ! perform molecular analysis at every 'this many' timesteps
-dipole_anal 0 ! 1: calculate a electric dipole moment of the system
-freq_dipole_anal 1 ! calculate electric dipole moment at every 'this many' steps
-diffusion_coef 0 ! 1: calculate diffusion coefficient of the system
-freq_diffusion_coef 1 ! calculate diffusion coefficient at every 'this many' steps
-restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
diff --git a/test_harness/control_water_6540_serial b/test_harness/control_water_6540_serial
deleted file mode 100644
index edeb3b50..00000000
--- a/test_harness/control_water_6540_serial
+++ /dev/null
@@ -1,68 +0,0 @@
-simulation_name water_6540_notab_nve_qeq_serial ! output files will carry this name + their specific extension
-ensemble_type 0 ! 0: NVE, 1: Berendsen NVT, 2: nose-Hoover NVT, 3: semi-isotropic NPT, 4: isotropic NPT, 5: anisotropic NPT
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
-
-reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
-restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
-tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
-remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
-
-nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
-thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
-
-charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
-cm_q_net 0.0 ! net system charge
-cm_solver_type 0 ! iterative linear solver for charge method: 0 = GMRES(k), 1 = GMRES_H(k), 2 = CG, 3 = SDM
-cm_solver_max_iters 20 ! max solver iterations
-cm_solver_restart 100 ! inner iterations of before restarting (GMRES(k)/GMRES_H(k))
-cm_solver_q_err 1e-6 ! relative residual norm threshold used in solver
-cm_domain_sparsity 1.0 ! scalar for scaling cut-off distance, used to sparsify charge matrix (between 0.0 and 1.0)
-cm_init_guess_extrap1 3 ! order of spline extrapolation for initial guess (s)
-cm_init_guess_extrap2 2 ! order of spline extrapolation for initial guess (t)
-cm_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
-cm_solver_pre_comp_refactor 1000 ! number of steps before recomputing preconditioner
-cm_solver_pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (FG-ILUT)
-cm_solver_pre_comp_sai_thres 0.1 ! ratio of charge matrix NNZ's used to compute preconditioner (SAI)
-cm_solver_pre_app_type 1 ! method used to apply preconditioner (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_app_jacobi_iters 50 ! num. Jacobi iterations used for applying precondition (ICHOLT/ILUT/FG-ILUT)
-
-temp_init 0.0 ! desired initial temperature of the simulated system
-temp_final 300.0 ! desired final temperature of the simulated system
-t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
-t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
-t_rate -100.0 ! in K
-t_freq 4.0 ! in ps
-
-pressure 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 5000.00 ! in fs, pressure inertia parameter
-compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
-press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
-
-geo_format 1 ! 0: custom, 1: pdb, 2: bgf
-write_freq 0 ! write trajectory after so many steps
-traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
-traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
-traj_title WATER_NVE ! (no white spaces)
-atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
-atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
-atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
-bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
-angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
-test_forces 0 ! 0: normal run, 1: at every timestep print each force type into a different file
-
-molec_anal 0 ! 1: outputs newly formed molecules as the simulation progresses
-freq_molec_anal 0 ! perform molecular analysis at every 'this many' timesteps
-dipole_anal 0 ! 1: calculate a electric dipole moment of the system
-freq_dipole_anal 1 ! calculate electric dipole moment at every 'this many' steps
-diffusion_coef 0 ! 1: calculate diffusion coefficient of the system
-freq_diffusion_coef 1 ! calculate diffusion coefficient at every 'this many' steps
-restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
diff --git a/test_harness/control_water_78480_serial b/test_harness/control_water_78480_serial
deleted file mode 100644
index dbc5080f..00000000
--- a/test_harness/control_water_78480_serial
+++ /dev/null
@@ -1,68 +0,0 @@
-simulation_name water_78480_notab_nve_qeq_serial ! output files will carry this name + their specific extension
-ensemble_type 0 ! 0: NVE, 1: Berendsen NVT, 2: nose-Hoover NVT, 3: semi-isotropic NPT, 4: isotropic NPT, 5: anisotropic NPT
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
-
-reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
-restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
-tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
-remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
-
-nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
-thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
-
-charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
-cm_q_net 0.0 ! net system charge
-cm_solver_type 0 ! iterative linear solver for charge method: 0 = GMRES(k), 1 = GMRES_H(k), 2 = CG, 3 = SDM
-cm_solver_max_iters 20 ! max solver iterations
-cm_solver_restart 100 ! inner iterations of before restarting (GMRES(k)/GMRES_H(k))
-cm_solver_q_err 1e-6 ! relative residual norm threshold used in solver
-cm_domain_sparsity 1.0 ! scalar for scaling cut-off distance, used to sparsify charge matrix (between 0.0 and 1.0)
-cm_init_guess_extrap1 3 ! order of spline extrapolation for initial guess (s)
-cm_init_guess_extrap2 2 ! order of spline extrapolation for initial guess (t)
-cm_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
-cm_solver_pre_comp_refactor 1000 ! number of steps before recomputing preconditioner
-cm_solver_pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (FG-ILUT)
-cm_solver_pre_comp_sai_thres 0.1 ! ratio of charge matrix NNZ's used to compute preconditioner (SAI)
-cm_solver_pre_app_type 1 ! method used to apply preconditioner (ICHOLT/ILUT/FG-ILUT)
-cm_solver_pre_app_jacobi_iters 50 ! num. Jacobi iterations used for applying precondition (ICHOLT/ILUT/FG-ILUT)
-
-temp_init 0.0 ! desired initial temperature of the simulated system
-temp_final 300.0 ! desired final temperature of the simulated system
-t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
-t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
-t_rate -100.0 ! in K
-t_freq 4.0 ! in ps
-
-pressure 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 5000.00 ! in fs, pressure inertia parameter
-compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
-press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
-
-geo_format 0 ! 0: custom, 1: pdb, 2: bgf
-write_freq 0 ! write trajectory after so many steps
-traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
-traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
-traj_title WATER_NVE ! (no white spaces)
-atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
-atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
-atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
-bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
-angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
-test_forces 0 ! 0: normal run, 1: at every timestep print each force type into a different file
-
-molec_anal 0 ! 1: outputs newly formed molecules as the simulation progresses
-freq_molec_anal 0 ! perform molecular analysis at every 'this many' timesteps
-dipole_anal 0 ! 1: calculate a electric dipole moment of the system
-freq_dipole_anal 1 ! calculate electric dipole moment at every 'this many' steps
-diffusion_coef 0 ! 1: calculate diffusion coefficient of the system
-freq_diffusion_coef 1 ! calculate diffusion coefficient at every 'this many' steps
-restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
diff --git a/test_harness/submit_short_jobs.bash b/test_harness/submit_short_jobs.bash
index 4c44a8b7..bbfa259a 100755
--- a/test_harness/submit_short_jobs.bash
+++ b/test_harness/submit_short_jobs.bash
@@ -1,17 +1,31 @@
#!/bin/bash
+# submit job scripts of specified type
+#
+# inputs: 1) job_type, 2) data set
function submit_job_serial
{
- SIM_NAME="spuremd-${4}"
- qsub -l "walltime=${JOB_TIME},nodes=${JOB_NODES}:ppn=${JOB_PPN},feature=${JOB_FEATURE},mem=${JOB_MEM}" \
- -o "${SIM_NAME}" -j oe << EOF
-#!/bin/bash
-module purge
-module load GNU/6.2 MKL/11.2
-cd "\${PBS_O_WORKDIR}"
-../sPuReMD/bin/spuremd "${1}" "${2}" "${3}"
-EOF
+ python3 ../../tools/run_sim.py submit_jobs \
+ -b "../../sPuReMD/bin/spuremd" \
+ -p ensemble_type "0" \
+ -p nsteps "100" \
+ -p tabulate_long_range "0" \
+ -p charge_method "0" \
+ -p cm_solver_type "0" \
+ -p cm_solver_max_iters "50" \
+ -p cm_solver_restart "200" \
+ -p cm_solver_q_err "1e-6" \
+ -p cm_domain_sparsity "1.0" \
+ -p cm_solver_pre_comp_type "1" \
+ -p cm_solver_pre_comp_refactor "10000" \
+ -p cm_solver_pre_comp_droptol "0.0" \
+ -p cm_solver_pre_comp_sweeps "3" \
+ -p cm_solver_pre_comp_sai_thres "0.1" \
+ -p cm_solver_pre_app_type "0" \
+ -p cm_solver_pre_app_jacobi_iters "30" \
+ -p threads "1" \
+ "${1}" "${2}"
}
@@ -43,74 +57,83 @@ EOF
}
-############
-# Serial Runs #
-############
+# serial jobs (spuremd)
JOB_TIME="03:59:00"
JOB_NODES="1"
JOB_PPN="1"
JOB_FEATURE="lac"
JOB_MEM="120gb"
-
-sub_job_serial "../data/benchmarks/metal/zno_6912.pdb" \
- "../data/benchmarks/metal/ffield.zno" \
- "control_zno_6912_serial" \
- "zno_6912_serial"
-
-sub_job_serial "../data/benchmarks/silica/silica_6000.pdb" \
- "../data/benchmarks/silica/ffield-bio" \
- "control_silica_6000_serial" \
- "silica_6000_serial"
-
-sub_job_serial "../data/benchmarks/water/water_6540.pdb" \
- "../data/benchmarks/water/ffield.water" \
- "control_water_6540_serial" \
- "water_6540_serial"
-
-############
-# MPI Runs #
-############
-JOB_TIME="03:59:00"
-JOB_NODES="1"
-JOB_PPN="2"
-JOB_FEATURE="lac"
-JOB_MEM="120gb"
-
-sub_job_mpi "../data/benchmarks/metal/zno_6912.pdb"
- "../data/benchmarks/metal/ffield.zno" \
- "control_zno_6912_mpi" \
- "zno_6912_mpi"
-
-sub_job_mpi "../data/benchmarks/silica/silica_6000.pdb" \
- "../data/benchmarks/silica/ffield-bio" \
- "control_silica_6000_mpi" \
- "silica_6000_mpi"
-
-sub_job_mpi "../data/benchmarks/water/water_6540.pdb" \
- "../data/benchmarks/water/ffield.water" \
- "control_water_6540_mpi" \
- "water_6540_mpi"
-
-################
-# MPI-GPU Runs #
-################
-JOB_TIME="03:59:00"
-JOB_NODES="2"
-JOB_PPN="1"
-JOB_FEATURE="lac"
-JOB_MEM="120gb"
-
-sub_job_mpi_gpu "../data/benchmarks/metal/zno_6912.pdb" \
- "../data/benchmarks/metal/ffield.zno"
- "control_zno_6912_mpi_gpu" \
- "zno_6912_mpi_gpu"
-
-sub_job_mpi_gpu "../data/benchmarks/silica/silica_6000.pdb" \
- "../data/benchmarks/silica/ffield-bio" \
- "control_silica_6000_mpi_gpu" \
- "silica_6000_mpi_gpu"
-
-sub_job_mpi_gpu "../data/benchmarks/water/water_6540.pdb" \
- "../data/benchmarks/water/ffield.water" \
- "control_water_6540_mpi_gpu" \
- "water_6540_mpi_gpu"
+DATA_DIR="serial"
+
+if [ ! -d "${DATA_DIR}" ]; then
+ mkdir "${DATA_DIR}"
+fi
+pushd "${DATA_DIR}" &> /dev/null
+
+submit_job_serial "slurm" "zno_6912"
+
+submit_job_serial "slurm" "silica_6000"
+
+submit_job_serial "slurm" "water_6540"
+
+popd &> /dev/null
+
+## mpi jobs (puremd)
+#JOB_TIME="03:59:00"
+#JOB_NODES="1"
+#JOB_PPN="2"
+#JOB_FEATURE="lac"
+#JOB_MEM="120gb"
+#DATA_DIR="mpi"
+#
+#if [ ! -d "${DATA_DIR}" ]; then
+# mkdir "${DATA_DIR}"
+#fi
+#pushd "${DATA_DIR}" &> /dev/null
+#
+#submit_job_mpi "../data/benchmarks/metal/zno_6912.pdb"
+# "../data/benchmarks/metal/ffield.zno" \
+# "control_zno_6912_mpi" \
+# "zno_6912_mpi"
+#
+#submit_job_mpi "../data/benchmarks/silica/silica_6000.pdb" \
+# "../data/benchmarks/silica/ffield-bio" \
+# "control_silica_6000_mpi" \
+# "silica_6000_mpi"
+#
+#submit_job_mpi "../data/benchmarks/water/water_6540.pdb" \
+# "../data/benchmarks/water/ffield.water" \
+# "control_water_6540_mpi" \
+# "water_6540_mpi"
+#
+#popd &> /dev/null
+#
+## mpi+gpu jobs (pg-puremd)
+#JOB_TIME="03:59:00"
+#JOB_NODES="2"
+#JOB_PPN="1"
+#JOB_FEATURE="lac"
+#JOB_MEM="120gb"
+#DATA_DIR="mpi_gpu"
+#
+#if [ ! -d "${DATA_DIR}" ]; then
+# mkdir "${DATA_DIR}"
+#fi
+#pushd "${DATA_DIR}" &> /dev/null
+#
+#submit_job_mpi_gpu "../data/benchmarks/metal/zno_6912.pdb" \
+# "../data/benchmarks/metal/ffield.zno"
+# "control_zno_6912_mpi_gpu" \
+# "zno_6912_mpi_gpu"
+#
+#submit_job_mpi_gpu "../data/benchmarks/silica/silica_6000.pdb" \
+# "../data/benchmarks/silica/ffield-bio" \
+# "control_silica_6000_mpi_gpu" \
+# "silica_6000_mpi_gpu"
+#
+#submit_job_mpi_gpu "../data/benchmarks/water/water_6540.pdb" \
+# "../data/benchmarks/water/ffield.water" \
+# "control_water_6540_mpi_gpu" \
+# "water_6540_mpi_gpu"
+#
+#popd &> /dev/null
diff --git a/tools/run_sim.py b/tools/run_sim.py
index e9150086..cc4480c6 100644
--- a/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -19,47 +19,91 @@ class TestCase():
self.__result_file = result_file
self.__control_regexes = { \
'name': lambda l, x: sub(
- r'(?P<key>simulation_name\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>simulation_name\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'ensemble_type': lambda l, x: sub(
- r'(?P<key>ensemble_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>ensemble_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'nsteps': lambda l, x: sub(
- r'(?P<key>nsteps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>nsteps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'dt': lambda l, x: sub(
+ r'^(?P<key>dt\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'periodic_boundaries': lambda l, x: sub(
+ r'^(?P<key>periodic_boundaries\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'reposition_atoms': lambda l, x: sub(
+ r'^(?P<key>reposition_atoms\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'remove_CoM_vel': lambda l, x: sub(
+ r'^(?P<key>remove_CoM_vel\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'reneighbor': lambda l, x: sub(
+ r'^(?P<key>reneighbor\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'update_energy_freq': lambda l, x: sub(
+ r'^(?P<key>update_energy_freq\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'tabulate_long_range': lambda l, x: sub(
- r'(?P<key>tabulate_long_range\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>tabulate_long_range\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'vlist_buffer': lambda l, x: sub(
+ r'^(?P<key>vlist_buffer\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'nbrhood_cutoff': lambda l, x: sub(
+ r'^(?P<key>nbrhood_cutoff\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'hbond_cutoff': lambda l, x: sub(
+ r'^(?P<key>hbond_cutoff\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'thb_cutoff': lambda l, x: sub(
+ r'^(?P<key>thb_cutoff\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'bond_graph_cutoff': lambda l, x: sub(
+ r'^(?P<key>bond_graph_cutoff\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'charge_method': lambda l, x: sub(
- r'(?P<key>charge_method\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>charge_method\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_q_net': lambda l, x: sub(
- r'(?P<key>cm_q_net\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_q_net\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_type': lambda l, x: sub(
- r'(?P<key>cm_solver_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_max_iters': lambda l, x: sub(
- r'(?P<key>cm_solver_max_iters\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_max_iters\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_restart': lambda l, x: sub(
- r'(?P<key>cm_solver_restart\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_restart\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_q_err': lambda l, x: sub(
- r'(?P<key>cm_solver_q_err\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_q_err\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_domain_sparsity': lambda l, x: sub(
- r'(?P<key>cm_domain_sparsity\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_domain_sparsity\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_init_guess_extrap1': lambda l, x: sub(
- r'(?P<key>cm_init_guess_extrap1\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_init_guess_extrap1\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_init_guess_extrap2': lambda l, x: sub(
- r'(?P<key>cm_init_guess_extrap2\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_init_guess_extrap2\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_pre_comp_type': lambda l, x: sub(
- r'(?P<key>cm_solver_pre_comp_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_pre_comp_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_pre_comp_droptol': lambda l, x: sub(
- r'(?P<key>cm_solver_pre_comp_droptol\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_pre_comp_droptol\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_pre_comp_refactor': lambda l, x: sub(
- r'(?P<key>cm_solver_pre_comp_refactor\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_pre_comp_refactor\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_pre_comp_sweeps': lambda l, x: sub(
- r'(?P<key>cm_solver_pre_comp_sweeps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_pre_comp_sweeps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_pre_comp_sai_thres': lambda l, x: sub(
- r'(?P<key>cm_solver_pre_comp_sai_thres\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_pre_comp_sai_thres\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_pre_app_type': lambda l, x: sub(
- r'(?P<key>cm_solver_pre_app_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_pre_app_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'cm_solver_pre_app_jacobi_iters': lambda l, x: sub(
- r'(?P<key>cm_solver_pre_app_jacobi_iters\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>cm_solver_pre_app_jacobi_iters\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'geo_format': lambda l, x: sub(
- r'(?P<key>geo_format\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ r'^(?P<key>geo_format\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'temp_init': lambda l, x: sub(
+ r'^(?P<key>temp_init\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'temp_final': lambda l, x: sub(
+ r'^(?P<key>temp_final\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 't_mass': lambda l, x: sub(
+ r'^(?P<key>t_mass\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 't_mode': lambda l, x: sub(
+ r'^(?P<key>t_mode\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 't_rate': lambda l, x: sub(
+ r'^(?P<key>t_rate\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 't_freq': lambda l, x: sub(
+ r'^(?P<key>t_freq\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'pressure': lambda l, x: sub(
+ r'^(?P<key>pressure\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'p_mass': lambda l, x: sub(
+ r'^(?P<key>p_mass\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'pt_mass': lambda l, x: sub(
+ r'^(?P<key>pt_mass\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'compress': lambda l, x: sub(
+ r'^(?P<key>compress\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'press_mode': lambda l, x: sub(
+ r'^(?P<key>press_mode\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
}
self.__params['geo_format'] = geo_format
self.__min_step = min_step
@@ -83,15 +127,17 @@ dt 0.25 ! time step in fs
periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
+remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
+reneighbor 1 ! frequency to recompute Verlet lists
restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
-tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
energy_update_freq 1
-remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
+tabulate_long_range 0 ! denotes the granularity of long range tabulation, 0 means no tabulation
-nbrhood_cutoff 5.0 ! near neighbors cutoff for bond calculations (Angstroms)
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
+vlist_buffer 0.0 ! skim distance on top of non-bonded interaction cutoff (Angstroms)
+nbrhood_cutoff 5.0 ! cutoff distance for bond interaction (Angstroms)
+hbond_cutoff 7.5 ! cutoff distance for hydrogen bond interactions (Angstroms)
thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
+bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
cm_q_net 0.0 ! net system charge
@@ -143,7 +189,7 @@ freq_diffusion_coef 1 ! calculate diffusion coefficien
restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
+restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps\
"""
# substitute key-value pairs in the text of the control file
@@ -207,10 +253,8 @@ restart_freq 0 ! 0: do not output any restart f
if proc_handle.returncode < 0:
print("WARNING: process terminated with code {0}".format(proc_handle.returncode))
- print('stdout:')
- print(stdout)
- print('stderr:')
- print(stderr)
+ print('stdout:\n{0}'.format(stdout), end='')
+ print('stderr:\n{0}'.format(stderr), end='')
if path.exists(temp_file):
remove(temp_file)
@@ -315,8 +359,8 @@ restart_freq 0 ! 0: do not output any restart f
def _build_slurm_script(self, binary, param_values):
from os import path
- # back up two directory levels
- base_dir = path.dirname(path.dirname(path.dirname(binary)))
+ # remove executable and back up two directory levels
+ base_dir = path.dirname(path.dirname(path.dirname(path.abspath(binary))))
job_script = """\
#!/bin/bash -login
@@ -346,8 +390,8 @@ python3 {0}/tools/run_sim.py run_md \\
def _build_pbs_script(self, binary, param_values):
from os import path
- # back up two directory levels
- base_dir = path.dirname(path.dirname(path.dirname(binary)))
+ # remove executable and back up two directory levels
+ base_dir = path.dirname(path.dirname(path.dirname(path.abspath(binary))))
job_script = """\
#!/bin/bash -login
@@ -390,12 +434,10 @@ python3 {0}/tools/run_sim.py run_md \\
if proc_handle.returncode < 0:
print("WARNING: process terminated with code {0}".format(proc_handle.returncode))
- print('stdout:')
- print(stdout)
- print('stderr:')
- print(stderr)
+ print('stdout:\n{0}'.format(stdout), end='')
+ print('stderr:\n{0}'.format(stderr), end='')
else:
- print(stdout)
+ print(stdout, end='')
if __name__ == '__main__':
@@ -404,12 +446,13 @@ if __name__ == '__main__':
from sys import exit
def setup_parser():
- DATA = [ \
+ DATA_SETS = [ \
'bilayer_56800', 'bilayer_340800', \
'dna_19733', \
'petn_48256', \
'silica_6000', 'silica_72000', 'silica_300000', \
'water_6540', 'water_78480', 'water_327000', \
+ 'zno_6912', \
]
JOB_TYPES = ['pbs', 'slurm']
@@ -424,7 +467,7 @@ if __name__ == '__main__':
run_md_parser.add_argument('-p', '--params', metavar='params', action='append', default=None, nargs=2,
help='Paramater name and value pairs for the simulation, with multiple values comma delimited.')
run_md_parser.add_argument('data_sets', nargs='+',
- choices=DATA, help='Data sets for which to run simulations.')
+ choices=DATA_SETS, help='Data sets for which to run simulations.')
run_md_parser.set_defaults(func=run_md)
parse_results_parser.add_argument('-f', '--out_file', metavar='out_file', default=None, nargs=1,
@@ -436,7 +479,7 @@ if __name__ == '__main__':
parse_results_parser.add_argument('-x', '--max_step', metavar='max_step', default=None, nargs=1,
help='Maxiumum simulation step for aggregating results.')
parse_results_parser.add_argument('data_sets', nargs='+',
- choices=DATA, help='Data sets for which to parse results.')
+ choices=DATA_SETS, help='Data sets for which to parse results.')
parse_results_parser.set_defaults(func=parse_results)
submit_jobs_parser.add_argument('-b', '--binary', metavar='binary', default=None, nargs=1,
@@ -446,7 +489,7 @@ if __name__ == '__main__':
submit_jobs_parser.add_argument('job_script_type', nargs=1,
choices=JOB_TYPES, help='Type of job script.')
submit_jobs_parser.add_argument('data_sets', nargs='+',
- choices=DATA, help='Data sets for which to run simulations.')
+ choices=DATA_SETS, help='Data sets for which to run simulations.')
submit_jobs_parser.set_defaults(func=submit_jobs)
return parser
@@ -457,7 +500,18 @@ if __name__ == '__main__':
control_params_dict = {
'ensemble_type': ['0'],
'nsteps': ['20'],
+ 'dt': ['0.25'],
+ 'periodic_boundaries': ['1'],
+ 'reposition_atoms': ['0'],
+ 'remove_CoM_vel': ['500'],
+ 'reneighbor': ['1'],
+ 'update_energy_freq': ['1'],
'tabulate_long_range': ['0'],
+ 'vlist_buffer': ['0.0'],
+ 'nbrhood_cutoff': ['5.0'],
+ 'hbond_cutoff': ['0.0'],
+ 'thb_cutoff': ['0.001'],
+ 'bond_graph_cutoff': ['0.3'],
'charge_method': ['0'],
'cm_q_net': ['0.0'],
'cm_solver_type': ['0'],
@@ -476,6 +530,17 @@ if __name__ == '__main__':
'cm_solver_pre_app_jacobi_iters': ['30'],
'threads': ['1'],
'geo_format': [],
+ 'temp_init': ['0.0'],
+ 'temp_final': ['300.0'],
+ 't_mass': ['0.166666'],
+ 't_mode': ['0'],
+ 't_rate': ['-100.0'],
+ 't_freq': ['4.0'],
+ 'pressure': ['0.000101325'],
+ 'p_mass': ['5000.0'],
+ 'pt_mass': ['5000.0'],
+ 'compress': ['0.008134'],
+ 'press_mode': ['0'],
}
return control_dir, data_dir, control_params_dict
@@ -582,16 +647,27 @@ if __name__ == '__main__':
result_header = header_str, result_body_fmt=body_fmt_str,
geo_format=['1'], result_file=result_file,
min_step=min_step, max_step=max_step))
+ if 'zno_6912' in data_sets:
+ test_cases.append(
+ TestCase('zno_6912',
+ path.join(data_dir, 'metal/zno_6912.pdb'),
+ path.join(data_dir, 'metal/ffield.zno'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['1'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
return test_cases
def run_md(args):
- base_dir = getcwd()
- control_dir, data_dir, control_params_dict = setup_defaults(base_dir)
-
if args.binary:
binary = args.binary[0]
+ # remove executable and back up two directory levels
+ base_dir = path.dirname(path.dirname(path.dirname(path.abspath(binary))))
+ control_dir, data_dir, control_params_dict = setup_defaults(base_dir)
else:
+ base_dir = getcwd()
binary = path.join(base_dir, 'sPuReMD/bin/spuremd')
# overwrite default control file parameter values if supplied via command line args
@@ -640,12 +716,13 @@ if __name__ == '__main__':
test.parse_results()
def submit_jobs(args):
- base_dir = getcwd()
- control_dir, data_dir, control_params_dict = setup_defaults(base_dir)
-
if args.binary:
binary = args.binary[0]
+ # remove executable and back up two directory levels
+ base_dir = path.dirname(path.dirname(path.dirname(path.abspath(binary))))
+ control_dir, data_dir, control_params_dict = setup_defaults(base_dir)
else:
+ base_dir = getcwd()
binary = path.join(base_dir, 'sPuReMD/bin/spuremd')
# overwrite default control file parameter values if supplied via command line args
--
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