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 d1646173b69744d7d8076474a39a23844d60b2e7..0000000000000000000000000000000000000000 --- 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 35af73ed3c3eace00790feee2bf49d6ea624234f..0000000000000000000000000000000000000000 --- 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 2c6aa7e544e05a3ab64096832a3f374411bb6a85..ea03ff53ddbbdb700435423667a0aed5b162afe3 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 0000000000000000000000000000000000000000..7087989c6064cafb856fdeb9bc5ca3045df771d2 --- /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 0000000000000000000000000000000000000000..a0efb8175662970a57d471b70b3f7d565069e4ca --- /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 0000000000000000000000000000000000000000..a3cc7de048e77e0645f05e26cda2c3a2e6598c79 --- /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 3e1d10cf948ac067243dff11028f831ea037b81a..73ba28e61b4c2db37ee864b0bb06b92de649bbee 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 0000000000000000000000000000000000000000..6fc327feaa9918d06b0c51fc0449fd6d98017514 --- /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 42746753ee874b10845d905188a888620d4b9f0c..23dceb7d450287fa5eb4626b10c2d10f5108fc6a 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 0000000000000000000000000000000000000000..5b4cee39df8af543e4b6ce7cc08197736a119f88 --- /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 d6241044c54ecf533cb6930d9de9124166eac3fa..e9e69cb6ac607be093b83ddd3c104ceb410c2dd8 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 0000000000000000000000000000000000000000..1990d37a00dc26da078c331f03eafd62167ca784 --- /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 c5019d4864d885f9d98424eaf1e1a17e7962df52..3a3615fed6c16184a65e04fecfbbdbe8de08305d 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 0000000000000000000000000000000000000000..e895ac170589382857d9b0fcc6b153a0cc553143 --- /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 d1ec1204006344110808f7e1871237956da2e6b4..a9113f204c2ef52ca6da469dd97aaa0974c14aea 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 0000000000000000000000000000000000000000..edeb3b506ee96ab12e6274724616c3551bac8e38 --- /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 98a870ddabcf2da0cfac6c8d85107fa05d96cfd6..87ef23ccef74f56dc22f2ebb64eeebde51df7d44 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 0000000000000000000000000000000000000000..dbc5080fe5c53b154c10af2379bc38c143fbe1ae --- /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 3d97cdb99821411ba421abcab3a2d79ae1b0bb6a..41de86640994e1270517bf2b62dcb245a6422b6d 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 b835ccf4ad9564d5e1e864e8645279a673ebfaac..4c44a8b7fe3cbe50f0cc0c7c1229afcfa3d20ebe 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"