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Commit 85be1860 authored by Kurt A. O'Hearn's avatar Kurt A. O'Hearn
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Test: add MPI+GPU control files.

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test_harness/control_bilayer_340800_mpi
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View file @ 85be1860
simulation_name bilayer_340800_notab_nve_qeq_mpi ! output files will carry this name + their specific ext. 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) 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 nsteps 100 ! number of simulation steps
dt 0.10 ! time step in fs dt 0.10 ! time step in fs
proc_by_dim 1 1 2 ! distribution of processors by dimensions periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart 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 reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
reposition_atoms 1 ! 1:center of mass to center of box 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 reneighbor 1
vlist_buffer 0 vlist_buffer 0
nbrhood_cutoff 4.5 ! bond cutoff in A
hbond_cutoff 7.5 ! hbond cutoff in A nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
thb_cutoff 0.001 ! cutoff value for three body interactions bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
qeq_freq 1 ! frequency to update charges with QEq hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
q_err 1e-6 ! norm of the relative residual in QEq solve
qeq_freq 1 ! frequency to update charges with QEq
temp_init 0.01 ! initial temperature of the system q_err 1e-6 ! norm of the relative residual in QEq solve
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 temp_init 0.0 ! desired initial temperature of the simulated system
t_rate 5.0 ! in K temp_final 300.0 ! desired final temperature of the simulated system
t_freq 1.0 ! in ps t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
t_mode 2 ! 2: constant slope t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
t_rate -100.0 ! in K
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa t_freq 4.0 ! in ps
p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
write_freq 0 ! write trajectory after so many steps p_mass 5000.00 5000.00 5000.00 ! in fs, pressure inertia parameter
traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
traj_title micelle ! (no white spaces) press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
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 geo_format 1 ! 0: custom, 1: pdb, 2: bgf
atom_velocities 1 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file write_freq 0 ! write trajectory after so many steps
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file traj_title WATER_NVE ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps 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
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
test_harness/control_bilayer_340800_mpi_gpu
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View file @ 85be1860
simulation_name bilayer.340800_mpi_gpu ! output files will carry this name + their specific ext. simulation_name bilayer_340800_notab_nve_qeq_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) 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 nsteps 100 ! number of simulation steps
dt 0.10 ! time step in fs dt 0.10 ! time step in fs
proc_by_dim 2 2 2 ! distribution of processors by dimensions periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart proc_by_dim 1 1 2 ! distribution of processors by dimensions
gpus_per_node 2 ! GPUs per node
tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation geo_format 1 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
energy_update_freq 10
remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
reposition_atoms 1 ! 1:center of mass to center of box 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 reneighbor 1
vlist_buffer 0 vlist_buffer 0
nbrhood_cutoff 4.5 ! bond cutoff in A
hbond_cutoff 7.5 ! hbond cutoff in A nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
thb_cutoff 0.001 ! cutoff value for three body interactions bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
qeq_freq 1 ! frequency to update charges with QEq hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
q_err 1e-6 ! norm of the relative residual in QEq solve
qeq_freq 1 ! frequency to update charges with QEq
temp_init 0.01 ! initial temperature of the system q_err 1e-6 ! norm of the relative residual in QEq solve
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 temp_init 0.0 ! desired initial temperature of the simulated system
t_rate 5.0 ! in K temp_final 300.0 ! desired final temperature of the simulated system
t_freq 1.0 ! in ps t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
t_mode 2 ! 2: constant slope t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
t_rate -100.0 ! in K
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa t_freq 4.0 ! in ps
p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
write_freq 0 ! write trajectory after so many steps p_mass 5000.00 5000.00 5000.00 ! in fs, pressure inertia parameter
traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
traj_title micelle ! (no white spaces) press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
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 geo_format 1 ! 0: custom, 1: pdb, 2: bgf
atom_velocities 1 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file write_freq 0 ! write trajectory after so many steps
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file traj_title WATER_NVE ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps 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
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
test_harness/control_bilayer_56800_mpi_gpu 0 → 100644
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View file @ 85be1860
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
test_harness/control_silica_300000_mpi_gpu
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− 41
View file @ 85be1860
simulation_name silica.300000_mpi_gpu ! output files will carry this name + their specific ext. simulation_name silica_300000_notab_nve_qeq_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) 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 nsteps 100 ! number of simulation steps
dt 0.10 ! time step in fs dt 0.10 ! time step in fs
proc_by_dim 2 2 2 ! distribution of processors by dimensions periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart proc_by_dim 1 1 2 ! distribution of processors by dimensions
gpus_per_node 2 ! GPUs per node
tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
energy_update_freq 10
remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
reposition_atoms 1 ! 1:center of mass to center of box 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 reneighbor 1
vlist_buffer 0 vlist_buffer 0
nbrhood_cutoff 4.5 ! bond cutoff in A
hbond_cutoff 0 ! hbond cutoff in A nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
thb_cutoff 0.001 ! cutoff value for three body interactions bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
qeq_freq 1 ! frequency to update charges with QEq hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
q_err 1e-6 ! norm of the relative residual in QEq solve
qeq_freq 1 ! frequency to update charges with QEq
temp_init 0.01 ! initial temperature of the system q_err 1e-6 ! norm of the relative residual in QEq solve
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 temp_init 0.0 ! desired initial temperature of the simulated system
t_rate 5.0 ! in K temp_final 300.0 ! desired final temperature of the simulated system
t_freq 1.0 ! in ps t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
t_mode 2 ! 2: constant slope t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
t_rate -100.0 ! in K
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa t_freq 4.0 ! in ps
p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
write_freq 0 ! write trajectory after so many steps p_mass 5000.00 5000.00 5000.00 ! in fs, pressure inertia parameter
traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
traj_title micelle ! (no white spaces) press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
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 geo_format 1 ! 0: custom, 1: pdb, 2: bgf
atom_velocities 1 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file write_freq 0 ! write trajectory after so many steps
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file traj_title WATER_NVE ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps 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
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
test_harness/control_silica_6000_mpi_gpu 0 → 100644
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View file @ 85be1860
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
test_harness/control_silica_72000_mpi_gpu 0 → 100644
+ 50
− 0
View file @ 85be1860
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
test_harness/control_water_327000_mpi_gpu
+ 47
− 41
View file @ 85be1860
simulation_name water.327000_mpi_gpu ! output files will carry this name + their specific ext. simulation_name water_327000_notab_nve_qeq_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) 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 nsteps 100 ! number of simulation steps
dt 0.10 ! time step in fs dt 0.10 ! time step in fs
proc_by_dim 2 2 2 ! distribution of processors by dimensions periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart proc_by_dim 1 1 2 ! distribution of processors by dimensions
gpus_per_node 2 ! GPUs per node
tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
energy_update_freq 10
remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
reposition_atoms 1 ! 1:center of mass to center of box 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 reneighbor 1
vlist_buffer 0 vlist_buffer 0
nbrhood_cutoff 4.5 ! bond cutoff in A
hbond_cutoff 7.5 ! hbond cutoff in A nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations (Angstroms)
thb_cutoff 0.001 ! cutoff value for three body interactions bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
qeq_freq 1 ! frequency to update charges with QEq hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
q_err 1e-6 ! norm of the relative residual in QEq solve
qeq_freq 1 ! frequency to update charges with QEq
temp_init 0.01 ! initial temperature of the system q_err 1e-6 ! norm of the relative residual in QEq solve
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 temp_init 0.0 ! desired initial temperature of the simulated system
t_rate 5.0 ! in K temp_final 300.0 ! desired final temperature of the simulated system
t_freq 1.0 ! in ps t_mass 0.16666 ! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
t_mode 2 ! 2: constant slope t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
t_rate -100.0 ! in K
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa t_freq 4.0 ! in ps
p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
write_freq 0 ! write trajectory after so many steps p_mass 5000.00 5000.00 5000.00 ! in fs, pressure inertia parameter
traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
traj_title micelle ! (no white spaces) press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
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 geo_format 1 ! 0: custom, 1: pdb, 2: bgf
atom_velocities 1 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file write_freq 0 ! write trajectory after so many steps
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file traj_title WATER_NVE ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps 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
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
test_harness/control_water_6540_mpi_gpu 0 → 100644
+ 50
− 0
View file @ 85be1860
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
test_harness/control_water_78480_mpi_gpu 0 → 100644
+ 50
− 0
View file @ 85be1860
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
test_harness/control_zno_6912_mpi_gpu 0 → 100644
+ 45
− 0
View file @ 85be1860
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
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