From df5e305a3bebc4b2cffa9e17f92eb6164e18fe7d Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Mon, 1 Oct 2018 14:35:58 -0400
Subject: [PATCH] Test: add serial control files. Update MPI control files.
---
.../bilayer_340800_mpi_not_gpu_control | 44 ----------
test_harness/bilayer_56800_control | 44 ----------
...mpi_control => control_bilayer_340800_mpi} | 6 +-
...control => control_bilayer_340800_mpi_gpu} | 0
test_harness/control_bilayer_340800_serial | 68 +++++++++++++++
test_harness/control_bilayer_56800_mpi | 49 +++++++++++
test_harness/control_bilayer_56800_serial | 68 +++++++++++++++
test_harness/control_silica_300000_mpi | 87 ++++++++++---------
test_harness/control_silica_300000_serial | 68 +++++++++++++++
test_harness/control_silica_6000_mpi | 87 ++++++++++---------
test_harness/control_silica_6000_serial | 68 +++++++++++++++
test_harness/control_silica_72000_mpi | 87 ++++++++++---------
test_harness/control_silica_72000_serial | 68 +++++++++++++++
test_harness/control_water_327000_mpi | 87 ++++++++++---------
test_harness/control_water_327000_serial | 68 +++++++++++++++
test_harness/control_water_6540_mpi | 80 +++++++++--------
test_harness/control_water_6540_serial | 68 +++++++++++++++
test_harness/control_water_78480_mpi | 80 +++++++++--------
test_harness/control_water_78480_serial | 68 +++++++++++++++
test_harness/control_zno_6912_mpi | 4 +-
test_harness/submit_short_jobs.bash | 48 +++++-----
21 files changed, 890 insertions(+), 357 deletions(-)
delete mode 100644 test_harness/bilayer_340800_mpi_not_gpu_control
delete mode 100644 test_harness/bilayer_56800_control
rename test_harness/{bilayer_340800_mpi_control => control_bilayer_340800_mpi} (90%)
rename test_harness/{bilayer_340800_mpi_gpu_control => control_bilayer_340800_mpi_gpu} (100%)
create mode 100644 test_harness/control_bilayer_340800_serial
create mode 100644 test_harness/control_bilayer_56800_mpi
create mode 100644 test_harness/control_bilayer_56800_serial
create mode 100644 test_harness/control_silica_300000_serial
create mode 100644 test_harness/control_silica_6000_serial
create mode 100644 test_harness/control_silica_72000_serial
create mode 100644 test_harness/control_water_327000_serial
create mode 100644 test_harness/control_water_6540_serial
create mode 100644 test_harness/control_water_78480_serial
diff --git a/test_harness/bilayer_340800_mpi_not_gpu_control b/test_harness/bilayer_340800_mpi_not_gpu_control
deleted file mode 100644
index d1646173..00000000
--- a/test_harness/bilayer_340800_mpi_not_gpu_control
+++ /dev/null
@@ -1,44 +0,0 @@
-simulation_name bilayer.340800_mpi_not_gpu ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-proc_by_dim 2 2 2 ! distribution of processors by dimensions
-geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
-
-tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
-energy_update_freq 10
-remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
-reposition_atoms 1 ! 1:center of mass to center of box
-
-reneighbor 1
-vlist_buffer 0
-nbrhood_cutoff 4.5 ! bond cutoff in A
-hbond_cutoff 7.5 ! hbond cutoff in A
-thb_cutoff 0.001 ! cutoff value for three body interactions
-
-qeq_freq 1 ! frequency to update charges with QEq
-q_err 1e-6 ! norm of the relative residual in QEq solve
-
-temp_init 0.01 ! initial temperature of the system
-temp_final 300.0 ! final temperature of the system
-t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
-t_rate 5.0 ! in K
-t_freq 1.0 ! in ps
-t_mode 2 ! 2: constant slope
-
-pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
-
-write_freq 0 ! write trajectory after so many steps
-traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
-traj_title micelle ! (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 1 ! 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
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
-
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
diff --git a/test_harness/bilayer_56800_control b/test_harness/bilayer_56800_control
deleted file mode 100644
index 35af73ed..00000000
--- a/test_harness/bilayer_56800_control
+++ /dev/null
@@ -1,44 +0,0 @@
-simulation_name bilayer.56800 ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-proc_by_dim 1 1 2 ! distribution of processors by dimensions
-geo_format 1 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
-
-tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
-energy_update_freq 10
-remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
-reposition_atoms 1 ! 1:center of mass to center of box
-
-reneighbor 1
-vlist_buffer 0
-nbrhood_cutoff 4.5 ! bond cutoff in A
-hbond_cutoff 7.5 ! hbond cutoff in A
-thb_cutoff 0.001 ! cutoff value for three body interactions
-
-qeq_freq 1 ! frequency to update charges with QEq
-q_err 1e-6 ! norm of the relative residual in QEq solve
-
-temp_init 0.01 ! initial temperature of the system
-temp_final 300.0 ! final temperature of the system
-t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
-t_rate 5.0 ! in K
-t_freq 1.0 ! in ps
-t_mode 2 ! 2: constant slope
-
-pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
-
-write_freq 0 ! write trajectory after so many steps
-traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
-traj_title micelle ! (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 1 ! 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
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
-
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
diff --git a/test_harness/bilayer_340800_mpi_control b/test_harness/control_bilayer_340800_mpi
similarity index 90%
rename from test_harness/bilayer_340800_mpi_control
rename to test_harness/control_bilayer_340800_mpi
index 2c6aa7e5..ea03ff53 100644
--- a/test_harness/bilayer_340800_mpi_control
+++ b/test_harness/control_bilayer_340800_mpi
@@ -1,8 +1,8 @@
-simulation_name bilayer.340800_mpi ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
+simulation_name bilayer_340800_notab_nve_qeq_mpi ! output files will carry this name + their specific ext.
+ensemble_type 0 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
nsteps 100 ! number of simulation steps
dt 0.10 ! time step in fs
-proc_by_dim 2 2 2 ! distribution of processors by dimensions
+proc_by_dim 1 1 2 ! distribution of processors by dimensions
geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
diff --git a/test_harness/bilayer_340800_mpi_gpu_control b/test_harness/control_bilayer_340800_mpi_gpu
similarity index 100%
rename from test_harness/bilayer_340800_mpi_gpu_control
rename to test_harness/control_bilayer_340800_mpi_gpu
diff --git a/test_harness/control_bilayer_340800_serial b/test_harness/control_bilayer_340800_serial
new file mode 100644
index 00000000..7087989c
--- /dev/null
+++ b/test_harness/control_bilayer_340800_serial
@@ -0,0 +1,68 @@
+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_mpi b/test_harness/control_bilayer_56800_mpi
new file mode 100644
index 00000000..a0efb817
--- /dev/null
+++ b/test_harness/control_bilayer_56800_mpi
@@ -0,0 +1,49 @@
+simulation_name bilayer_56800_notab_nve_qeq_mpi ! output files will carry this name + their specific ext.
+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
+proc_by_dim 1 1 2 ! distribution of processors by dimensions
+geo_format 1 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
+
+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
+
+reneighbor 1
+vlist_buffer 0
+
+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)
+
+qeq_freq 1 ! frequency to update charges with QEq
+q_err 1e-6 ! norm of the relative residual in QEq solve
+
+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 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
+p_mass 5000.00 5000.00 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_method 1 ! 0: simple parallel I/O, 1: MPI I/O
+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
+
+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
new file mode 100644
index 00000000..a3cc7de0
--- /dev/null
+++ b/test_harness/control_bilayer_56800_serial
@@ -0,0 +1,68 @@
+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_mpi b/test_harness/control_silica_300000_mpi
index 3e1d10cf..73ba28e6 100644
--- a/test_harness/control_silica_300000_mpi
+++ b/test_harness/control_silica_300000_mpi
@@ -1,44 +1,49 @@
-simulation_name silica.300000_mpi ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-proc_by_dim 2 2 2 ! distribution of processors by dimensions
-geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
-
-tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
-energy_update_freq 10
-remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
-reposition_atoms 1 ! 1:center of mass to center of box
+simulation_name silica_300000_notab_nve_qeq_mpi ! output files will carry this name + their specific ext.
+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
+proc_by_dim 1 1 2 ! distribution of processors by dimensions
+geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
+
+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
reneighbor 1
vlist_buffer 0
-nbrhood_cutoff 4.5 ! bond cutoff in A
-hbond_cutoff 0 ! hbond cutoff in A
-thb_cutoff 0.001 ! cutoff value for three body interactions
-
-qeq_freq 1 ! frequency to update charges with QEq
-q_err 1e-6 ! norm of the relative residual in QEq solve
-
-temp_init 0.01 ! initial temperature of the system
-temp_final 300.0 ! final temperature of the system
-t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
-t_rate 5.0 ! in K
-t_freq 1.0 ! in ps
-t_mode 2 ! 2: constant slope
-
-pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
-
-write_freq 0 ! write trajectory after so many steps
-traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
-traj_title micelle ! (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 1 ! 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
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
-
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
+
+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)
+
+qeq_freq 1 ! frequency to update charges with QEq
+q_err 1e-6 ! norm of the relative residual in QEq solve
+
+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 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
+p_mass 5000.00 5000.00 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_method 1 ! 0: simple parallel I/O, 1: MPI I/O
+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
+
+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
new file mode 100644
index 00000000..6fc327fe
--- /dev/null
+++ b/test_harness/control_silica_300000_serial
@@ -0,0 +1,68 @@
+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_mpi b/test_harness/control_silica_6000_mpi
index 42746753..23dceb7d 100644
--- a/test_harness/control_silica_6000_mpi
+++ b/test_harness/control_silica_6000_mpi
@@ -1,44 +1,49 @@
-simulation_name silica.6000 ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-proc_by_dim 1 1 2 ! distribution of processors by dimensions
-geo_format 1 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
-
-tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
-energy_update_freq 10
-remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
-reposition_atoms 1 ! 1:center of mass to center of box
+simulation_name silica_6000_notab_nve_qeq_mpi ! output files will carry this name + their specific ext.
+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
+proc_by_dim 1 1 2 ! distribution of processors by dimensions
+geo_format 1 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
+
+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
reneighbor 1
vlist_buffer 0
-nbrhood_cutoff 4.5 ! bond cutoff in A
-hbond_cutoff 0 ! hbond cutoff in A
-thb_cutoff 0.001 ! cutoff value for three body interactions
-
-qeq_freq 1 ! frequency to update charges with QEq
-q_err 1e-6 ! norm of the relative residual in QEq solve
-
-temp_init 0.01 ! initial temperature of the system
-temp_final 300.0 ! final temperature of the system
-t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
-t_rate 5.0 ! in K
-t_freq 1.0 ! in ps
-t_mode 2 ! 2: constant slope
-
-pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
-
-write_freq 0 ! write trajectory after so many steps
-traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
-traj_title micelle ! (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 1 ! 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
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
-
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
+
+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)
+
+qeq_freq 1 ! frequency to update charges with QEq
+q_err 1e-6 ! norm of the relative residual in QEq solve
+
+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 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
+p_mass 5000.00 5000.00 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_method 1 ! 0: simple parallel I/O, 1: MPI I/O
+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
+
+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
new file mode 100644
index 00000000..5b4cee39
--- /dev/null
+++ b/test_harness/control_silica_6000_serial
@@ -0,0 +1,68 @@
+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_mpi b/test_harness/control_silica_72000_mpi
index d6241044..e9e69cb6 100644
--- a/test_harness/control_silica_72000_mpi
+++ b/test_harness/control_silica_72000_mpi
@@ -1,44 +1,49 @@
-simulation_name silica.72000 ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-proc_by_dim 1 1 2 ! distribution of processors by dimensions
-geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
-
-tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
-energy_update_freq 10
-remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
-reposition_atoms 1 ! 1:center of mass to center of box
+simulation_name silica_72000_notab_nve_qeq_mpi ! output files will carry this name + their specific ext.
+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
+proc_by_dim 1 1 2 ! distribution of processors by dimensions
+geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
+
+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
reneighbor 1
vlist_buffer 0
-nbrhood_cutoff 4.5 ! bond cutoff in A
-hbond_cutoff 0 ! hbond cutoff in A
-thb_cutoff 0.001 ! cutoff value for three body interactions
-
-qeq_freq 1 ! frequency to update charges with QEq
-q_err 1e-6 ! norm of the relative residual in QEq solve
-
-temp_init 0.01 ! initial temperature of the system
-temp_final 300.0 ! final temperature of the system
-t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
-t_rate 5.0 ! in K
-t_freq 1.0 ! in ps
-t_mode 2 ! 2: constant slope
-
-pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
-
-write_freq 0 ! write trajectory after so many steps
-traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
-traj_title micelle ! (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 1 ! 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
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
-
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
+
+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)
+
+qeq_freq 1 ! frequency to update charges with QEq
+q_err 1e-6 ! norm of the relative residual in QEq solve
+
+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 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
+p_mass 5000.00 5000.00 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_method 1 ! 0: simple parallel I/O, 1: MPI I/O
+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
+
+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
new file mode 100644
index 00000000..1990d37a
--- /dev/null
+++ b/test_harness/control_silica_72000_serial
@@ -0,0 +1,68 @@
+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_mpi b/test_harness/control_water_327000_mpi
index c5019d48..3a3615fe 100644
--- a/test_harness/control_water_327000_mpi
+++ b/test_harness/control_water_327000_mpi
@@ -1,44 +1,49 @@
-simulation_name water.327000_mpi ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-proc_by_dim 2 2 2 ! distribution of processors by dimensions
-geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
-
-tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
-energy_update_freq 10
-remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
-reposition_atoms 1 ! 1:center of mass to center of box
+simulation_name water_327000_notab_nve_qeq_mpi ! output files will carry this name + their specific ext.
+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
+proc_by_dim 1 1 2 ! distribution of processors by dimensions
+geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
+
+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
reneighbor 1
vlist_buffer 0
-nbrhood_cutoff 4.5 ! bond cutoff in A
-hbond_cutoff 7.5 ! hbond cutoff in A
-thb_cutoff 0.001 ! cutoff value for three body interactions
-
-qeq_freq 1 ! frequency to update charges with QEq
-q_err 1e-6 ! norm of the relative residual in QEq solve
-
-temp_init 0.01 ! initial temperature of the system
-temp_final 300.0 ! final temperature of the system
-t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
-t_rate 5.0 ! in K
-t_freq 1.0 ! in ps
-t_mode 2 ! 2: constant slope
-
-pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
-
-write_freq 0 ! write trajectory after so many steps
-traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
-traj_title micelle ! (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 1 ! 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
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
-
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
+
+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)
+
+qeq_freq 1 ! frequency to update charges with QEq
+q_err 1e-6 ! norm of the relative residual in QEq solve
+
+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 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
+p_mass 5000.00 5000.00 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_method 1 ! 0: simple parallel I/O, 1: MPI I/O
+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
+
+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
new file mode 100644
index 00000000..e895ac17
--- /dev/null
+++ b/test_harness/control_water_327000_serial
@@ -0,0 +1,68 @@
+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_mpi b/test_harness/control_water_6540_mpi
index d1ec1204..a9113f20 100644
--- a/test_harness/control_water_6540_mpi
+++ b/test_harness/control_water_6540_mpi
@@ -1,45 +1,49 @@
-simulation_name water.6540 ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-proc_by_dim 1 1 2 ! distribution of processors by dimensions
-geo_format 1 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
-
-tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
-energy_update_freq 10
-remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
-reposition_atoms 1 ! 1:center of mass to center of box
+simulation_name water_6540_notab_nve_qeq_mpi ! output files will carry this name + their specific ext.
+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
+proc_by_dim 1 1 2 ! distribution of processors by dimensions
+geo_format 1 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
+
+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
reneighbor 1
vlist_buffer 0
-nbrhood_cutoff 4.5 ! bond cutoff in A
-hbond_cutoff 7.5 ! hbond cutoff in A
-thb_cutoff 0.001 ! cutoff value for three body interactions
-qeq_freq 1 ! frequency to update charges with QEq
-q_err 1e-6 ! norm of the relative residual in QEq solve
+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)
-temp_init 0.01 ! initial temperature of the system
-temp_final 300.0 ! final temperature of the system
-t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
-t_rate 5.0 ! in K
-t_freq 1.0 ! in ps
-t_mode 2 ! 2: constant slope
+qeq_freq 1 ! frequency to update charges with QEq
+q_err 1e-6 ! norm of the relative residual in QEq solve
-pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
-
-write_freq 0 ! write trajectory after so many steps
-traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
-traj_title micelle ! (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 1 ! 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
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
-
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
+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 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
+p_mass 5000.00 5000.00 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_method 1 ! 0: simple parallel I/O, 1: MPI I/O
+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
+
+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
new file mode 100644
index 00000000..edeb3b50
--- /dev/null
+++ b/test_harness/control_water_6540_serial
@@ -0,0 +1,68 @@
+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_mpi b/test_harness/control_water_78480_mpi
index 98a870dd..87ef23cc 100644
--- a/test_harness/control_water_78480_mpi
+++ b/test_harness/control_water_78480_mpi
@@ -1,45 +1,49 @@
-simulation_name water.78480 ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
-nsteps 100 ! number of simulation steps
-dt 0.10 ! time step in fs
-proc_by_dim 1 1 2 ! distribution of processors by dimensions
-geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
-
-tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
-energy_update_freq 10
-remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
-reposition_atoms 1 ! 1:center of mass to center of box
+simulation_name water_78480_notab_nve_qeq_mpi ! output files will carry this name + their specific ext.
+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
+proc_by_dim 1 1 2 ! distribution of processors by dimensions
+geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
+
+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
reneighbor 1
vlist_buffer 0
-nbrhood_cutoff 4.5 ! bond cutoff in A
-hbond_cutoff 7.5 ! hbond cutoff in A
-thb_cutoff 0.001 ! cutoff value for three body interactions
-qeq_freq 1 ! frequency to update charges with QEq
-q_err 1e-6 ! norm of the relative residual in QEq solve
+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)
-temp_init 0.01 ! initial temperature of the system
-temp_final 300.0 ! final temperature of the system
-t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
-t_rate 5.0 ! in K
-t_freq 1.0 ! in ps
-t_mode 2 ! 2: constant slope
+qeq_freq 1 ! frequency to update charges with QEq
+q_err 1e-6 ! norm of the relative residual in QEq solve
-pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
-p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
-
-write_freq 0 ! write trajectory after so many steps
-traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
-traj_title micelle ! (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 1 ! 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
-
-restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
-restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
-
-bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
+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 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
+p_mass 5000.00 5000.00 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_method 1 ! 0: simple parallel I/O, 1: MPI I/O
+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
+
+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
new file mode 100644
index 00000000..dbc5080f
--- /dev/null
+++ b/test_harness/control_water_78480_serial
@@ -0,0 +1,68 @@
+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/control_zno_6912_mpi b/test_harness/control_zno_6912_mpi
index 3d97cdb9..41de8664 100644
--- a/test_harness/control_zno_6912_mpi
+++ b/test_harness/control_zno_6912_mpi
@@ -1,5 +1,5 @@
-simulation_name zno.6912 ! output files will carry this name + their specific ext.
-ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
+simulation_name zno_6912_notab_nve_qeq_mpi ! output files will carry this name + their specific ext.
+ensemble_type 0 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
nsteps 100 ! number of simulation steps
dt 0.10 ! time step in fs
proc_by_dim 1 1 2 ! distribution of processors by dimensions
diff --git a/test_harness/submit_short_jobs.bash b/test_harness/submit_short_jobs.bash
index b835ccf4..4c44a8b7 100755
--- a/test_harness/submit_short_jobs.bash
+++ b/test_harness/submit_short_jobs.bash
@@ -52,20 +52,20 @@ JOB_PPN="1"
JOB_FEATURE="lac"
JOB_MEM="120gb"
-sub_job_serial "../data/benchmarks/water/water_6540.pdb" \
- "../data/benchmarks/water/ffield.water" \
- "control_water_6540_serial" \
- "water_6540_serial"
+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/metal/zno_6912.pdb" \
- "../data/benchmarks/metal/ffield.zno" \
- "control_zno_6912_serial" \
- "zno_6912_serial"
+sub_job_serial "../data/benchmarks/water/water_6540.pdb" \
+ "../data/benchmarks/water/ffield.water" \
+ "control_water_6540_serial" \
+ "water_6540_serial"
############
# MPI Runs #
@@ -76,20 +76,20 @@ JOB_PPN="2"
JOB_FEATURE="lac"
JOB_MEM="120gb"
-sub_job_mpi "../data/benchmarks/water/water_6540.pdb" \
- "../data/benchmarks/water/ffield.water" \
- "control_water_6540_mpi" \
- "water_6540_mpi"
+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/metal/zno_6912.pdb"
- "../data/benchmarks/metal/ffield.zno" \
- "control_zno_6912_mpi" \
- "zno_6912_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 #
@@ -100,17 +100,17 @@ JOB_PPN="1"
JOB_FEATURE="lac"
JOB_MEM="120gb"
-sub_job_mpi_gpu "../data/benchmarks/water/water_6540.pdb" \
- "../data/benchmarks/water/ffield.water" \
- "control_water_6540_mpi_gpu" \
- "water_6540_mpi_gpu"
+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/metal/zno_6912.pdb" \
- "../data/benchmarks/metal/ffield.zno"
- "control_zno_6912_mpi_gpu" \
- "zno_6912_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"
--
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