diff --git a/environ/parallel_control b/environ/parallel_control index fe851fe6000268153f07738b2a9b1d2b429040d8..35ab6d0f1065f25ccafdcf67aee2f1e180c902fc 100644 --- a/environ/parallel_control +++ b/environ/parallel_control @@ -1,6 +1,6 @@ -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