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Commit df5e305a authored by Kurt A. O'Hearn's avatar Kurt A. O'Hearn
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Test: add serial control files. Update MPI control files.

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test_harness/bilayer_340800_mpi_not_gpu_control deleted 100644 → 0
+ 0
− 44
View file @ ffd8667c
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
test_harness/bilayer_56800_control deleted 100644 → 0
+ 0
− 44
View file @ ffd8667c
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
test_harness/bilayer_340800_mpi_control → test_harness/control_bilayer_340800_mpi
+ 3
− 3
View file @ df5e305a
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
......
test_harness/control_bilayer_340800_serial 0 → 100644
+ 68
− 0
View file @ df5e305a
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
test_harness/control_bilayer_56800_mpi 0 → 100644
+ 49
− 0
View file @ df5e305a
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
test_harness/control_bilayer_56800_serial 0 → 100644
+ 68
− 0
View file @ df5e305a
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
test_harness/control_silica_300000_mpi
+ 46
− 41
View file @ df5e305a
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
test_harness/control_silica_300000_serial 0 → 100644
+ 68
− 0
View file @ df5e305a
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
test_harness/control_silica_6000_mpi
+ 46
− 41
View file @ df5e305a
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
test_harness/control_silica_6000_serial 0 → 100644
+ 68
− 0
View file @ df5e305a
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
test_harness/control_silica_72000_mpi
+ 46
− 41
View file @ df5e305a
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
test_harness/control_silica_72000_serial 0 → 100644
+ 68
− 0
View file @ df5e305a
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
test_harness/control_water_327000_mpi
+ 46
− 41
View file @ df5e305a
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
test_harness/control_water_327000_serial 0 → 100644
+ 68
− 0
View file @ df5e305a
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
test_harness/control_water_6540_mpi
+ 42
− 38
View file @ df5e305a
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
test_harness/control_water_6540_serial 0 → 100644
+ 68
− 0
View file @ df5e305a
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
test_harness/control_water_78480_mpi
+ 42
− 38
View file @ df5e305a
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
test_harness/control_water_78480_serial 0 → 100644
+ 68
− 0
View file @ df5e305a
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
test_harness/control_zno_6912_mpi
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View file @ df5e305a
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
......
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