diff --git a/test_harness/control_bilayer_340800_mpi b/test_harness/control_bilayer_340800_mpi index ea03ff53ddbbdb700435423667a0aed5b162afe3..531101bf67c3a873448a1421fe01c14b6b4159e9 100644 --- a/test_harness/control_bilayer_340800_mpi +++ b/test_harness/control_bilayer_340800_mpi @@ -1,44 +1,49 @@ -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 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 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, 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 - -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_bilayer_340800_mpi_gpu b/test_harness/control_bilayer_340800_mpi_gpu index e084874f08e3a4876acabf2c0be785ccb38bdaf8..31983db0bd8ec2b133cf84b7c6493ff07c2f68d2 100644 --- a/test_harness/control_bilayer_340800_mpi_gpu +++ b/test_harness/control_bilayer_340800_mpi_gpu @@ -1,44 +1,50 @@ -simulation_name bilayer.340800_mpi_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 +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, 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 +gpus_per_node 2 ! GPUs per node +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 - -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_bilayer_56800_mpi_gpu b/test_harness/control_bilayer_56800_mpi_gpu new file mode 100644 index 0000000000000000000000000000000000000000..38a6d9f59c2fabc73f29798cbb19a9038d8b2eb8 --- /dev/null +++ b/test_harness/control_bilayer_56800_mpi_gpu @@ -0,0 +1,50 @@ +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 +gpus_per_node 2 ! GPUs per node +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_silica_300000_mpi_gpu b/test_harness/control_silica_300000_mpi_gpu index 08502ae0f5733eac91e48be2af517f354f93e580..88aea10d5f88a5bdfc279dc95096e2db04078bbb 100644 --- a/test_harness/control_silica_300000_mpi_gpu +++ b/test_harness/control_silica_300000_mpi_gpu @@ -1,44 +1,50 @@ -simulation_name silica.300000_mpi_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 +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 +gpus_per_node 2 ! GPUs per node +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_6000_mpi_gpu b/test_harness/control_silica_6000_mpi_gpu new file mode 100644 index 0000000000000000000000000000000000000000..2a63a8d11b48773f46c9f3106b44e7ac4903b056 --- /dev/null +++ b/test_harness/control_silica_6000_mpi_gpu @@ -0,0 +1,50 @@ +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 +gpus_per_node 2 ! GPUs per node +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_silica_72000_mpi_gpu b/test_harness/control_silica_72000_mpi_gpu new file mode 100644 index 0000000000000000000000000000000000000000..dc22b767e977c079bc2a799808a1b580789bf730 --- /dev/null +++ b/test_harness/control_silica_72000_mpi_gpu @@ -0,0 +1,50 @@ +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 +gpus_per_node 2 ! GPUs per node +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 ! 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_mpi_gpu b/test_harness/control_water_327000_mpi_gpu index 1cb38358a7d548c9aa1ba2fe86625842dce40c7d..1c6c1b9e91224d17e5b193cd2040256ba247e1e6 100644 --- a/test_harness/control_water_327000_mpi_gpu +++ b/test_harness/control_water_327000_mpi_gpu @@ -1,44 +1,50 @@ -simulation_name water.327000_mpi_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 +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 +gpus_per_node 2 ! GPUs per node +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_6540_mpi_gpu b/test_harness/control_water_6540_mpi_gpu new file mode 100644 index 0000000000000000000000000000000000000000..fd3ea0fec5063eba371ed084ee703fad885711b2 --- /dev/null +++ b/test_harness/control_water_6540_mpi_gpu @@ -0,0 +1,50 @@ +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 +gpus_per_node 2 ! GPUs per node +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_water_78480_mpi_gpu b/test_harness/control_water_78480_mpi_gpu new file mode 100644 index 0000000000000000000000000000000000000000..7a6889be9bfdefbd0cbc1327c4b4b5ef7d4cf5ea --- /dev/null +++ b/test_harness/control_water_78480_mpi_gpu @@ -0,0 +1,50 @@ +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 +gpus_per_node 2 ! GPUs per node +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 ! 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_zno_6912_mpi_gpu b/test_harness/control_zno_6912_mpi_gpu new file mode 100644 index 0000000000000000000000000000000000000000..8d6635257d74ec4b60fcbc7c73e6ad68cd986b78 --- /dev/null +++ b/test_harness/control_zno_6912_mpi_gpu @@ -0,0 +1,45 @@ +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 +gpus_per_node 2 ! GPUs per node +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 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