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Commit f1c9d000 authored by Kurt A. O'Hearn's avatar Kurt A. O'Hearn
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Update config file templates.

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environ/parallel_control
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View file @ f1c9d000
simulation_name water.6.112 ! 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 1
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 500 ! 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
simulation_name water.6.notab.111 ! 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 0.25 ! time step in fs
proc_by_dim 1 1 1 ! distribution of processors by dimensions
reposition_atoms 1 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
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 7.5 ! 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 0.01 ! desired initial temperature of the simulated system
temp_final 300.0 ! desired final temperature of the simulated system
t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
t_mode 2 ! 0: T-coupling only, 1: step-wise, 2: constant slope
t_rate 5.0 ! in K
t_freq 1.0 ! in ps
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
geo_format 1 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
write_freq 500 ! 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 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
environ/param.gpu.water
+ 6
− 6
View file @ f1c9d000
......@@ -9,10 +9,10 @@ tabulate_long_range 0 ! denotes the granularity of lon
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 5.0 ! near neighbors cutoff for bond calculations in A
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions
nbrhood_cutoff 5.0 ! 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_solver_type 0 ! iterative linear solver used for equilibration kernel (QEq)
qeq_solver_q_err 1e-6 ! relative residual norm threshold used in solver
......@@ -21,7 +21,7 @@ pre_comp_type 1 ! method used to compute QEq pre
pre_comp_refactor 100 ! nsteps to recompute preconditioner
pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation, if applicable
pre_comp_sweeps 3 ! sweeps to compute preconditioner (ILU_PAR)
pre_app_type 1 ! method used to apply QEq preconditioner
pre_app_type 1 ! method used to apply QEq preconditioner
pre_app_jacobi_iters 50 ! number of Jacobi iterations used for applying QEq precondition, if applicable
temp_init 0.0 ! desired initial temperature of the simulated system
......@@ -40,7 +40,7 @@ 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_NVT ! (no white spaces)
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
......
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