Skip to content
Snippets Groups Projects
Commit dd12580e authored by Kurt A. O'Hearn's avatar Kurt A. O'Hearn
Browse files

Fix template control file per BGF addition.

parent 00a8c164
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
environ/parallel_control
+ 18
− 18
View file @ dd12580e
simulation_name water_6540_notab_nve_qeq_111_mpi_gpu_probe ! 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 1000 ! number of simulation steps
simulation_name water.6.notab.111 ! 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 0.25 ! time step in fs
proc_by_dim 1 1 1 ! distribution of processors by dimensions
gpus_per_node 1 ! GPUs per node
......@@ -9,14 +9,14 @@ reposition_atoms 0 ! 0: just fit to periodic bounda
restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps
tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
energy_update_freq 1
remove_CoM_vel 0 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
reneighbor 1
vlist_buffer 0.0
vlist_buffer 0
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 7.5 ! cutoff distance for hydrogen bond interactions (Angstroms)
hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
charge_freq 1 ! frequency (sim step) at which atomic charges are computed
......@@ -24,19 +24,19 @@ cm_q_net 0.0 ! net system charge
cm_solver_type 2 ! iterative linear solver for charge method: 0 = GMRES, 1 = GMRES_H, 2 = CG, 3 = SDM
cm_solver_max_iters 1000 ! max solver iterations
cm_solver_restart 100 ! inner iterations of GMRES before restarting
cm_solver_q_err 1.0e-14 ! relative residual norm threshold used in solver
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_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
cm_solver_pre_comp_refactor 1 ! number of steps before recomputing preconditioner
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, if applicable
cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (ILU_PAR)
cm_solver_pre_app_type 1 ! method used to apply preconditioner
cm_solver_pre_app_jacobi_iters 50 ! number of Jacobi iterations used for applying precondition, if applicable
temp_init 0.0 ! desired initial temperature of the simulated system
temp_final 0.0 ! desired final temperature of the simulated system
t_mass 0.16666 ! thermal inertia parameter (fs): Nose-Hoover-NVT: 0.16666, NVP: 100.0, bNVT/iNPT/sNPT: 500.0
t_mode 0 ! 0: T-coupling only, 1: step-wise, 2: constant slope
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 ! thermal inertia parameter (fs): Nose-Hoover-NVT: 0.16666, NVP: 100.0, bNVT/iNPT/sNPT: 500.0
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
......@@ -47,18 +47,18 @@ press_mode 0 ! 0: internal + external pressur
geo_format 1 ! 0: custom 1: pdb (only if natoms < 100000) 2: bgf 3: ASCII restart 3: binary restart
write_freq 0 ! write trajectory after so many steps
traj_method 0 ! 0: simple parallel I/O, 1: MPI I/O
traj_title water_6540_notab_nve_qeq_111_mpi_gpu_probe ! (no white spaces)
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 0 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 0 ! 0: do not print angles, 1: print angles 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
dipole_anal 0 ! 1: calculate a electric dipole moment of the system
freq_dipole_anal 0 ! calculate electric dipole moment at every 'this many' steps
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 0 ! calculate diffusion coefficient at every 'this many' steps
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
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment