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card_file_formats
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card_file_formats
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!--------------------------------------------------------------------
! EXECUTION CONTROL
!
DRIVER = ! <== q_dynamics , avrg_confgs , Genetic_Alg , diagnostic , slice_{Cheb, AO, FSSH, CSDM} , MM_Dynamics
Survival = ! <== .TRUE. for any dynamics simulation
DP_Moment = ! <== .TRUE. or .FALSE. ; dipole moment fragment must be especified ad-hoc
QMMM = ! <== .TRUE. for Non-Adabatic simulations; couples electronic and nuclear dynamics
OPT_parms = ! <== .TRUE. for reading OPT_basis parameters from "opt_eht_parms.input"
ad_hoc = ! <== .TRUE. for using ad hoc tuning of parameters
rnd_seed = ! <== .TRUE. for undefined random_seed; .FALSE. (default) for pre-defined seed; relevant for FSSH and CSDM
DK_of_mixing = ! <== "local" (default) or "global"; relevant for FSSH and CSDM
Band_structure = ! <== .TRUE. for static band-structure calculations
!--------------------------------------------------------------------
! STRUCTURE-FILE input FORMAT
!
nuclear_matter = ! <== solvated_sys , extended_sys , MDynamics
file_type = ! <== structure or trajectory ; default = structure
file_format = ! <== xyz , pdb or vasp ; default = pdb
!--------------------------------------------------------------------
! generate copies of the system by reflection
!
nnx = 0 ; nny = 0 ! <== (nnx,nny) = (extended) REAL copies on each side
! Integers, keep format ; default = (0,0)
! Periodic Boundary Conditions
PBC = [ 0 , 0 , 0 ] ! <== PBC replicas : 1 = yes , 0 = no
! Integers, keep format , default = (0,0,0)
!--------------------------------------------------------------------
! QDynamics parameters
!
t_i = ! <== default = 0.d0
t_f = ! <== final time in PICOseconds (Real)
n_t = ! <== number of time steps (Integer)
n_part = ! <== # of particles to be propagated: default is e=1 , e+h=2 ; default = 2
hole_state = char*3:Integer ! <== char*3 = 3-letter fragment or residue ; Integer = MO of frag/res
! <== GROUND STATE calcs = 0 (ZERO)
! <== case STATIC & DP_calcs = hole state of special FMO
! <== case DYNAMIC = intial MO for < HOLE > wavepacket in DONOR fragment
electron_state = char*3:Integer ! <== char*3 = 3-letter fragment or residue ; Integer = MO of frag/res
! <== case STATIC & DP_calcs = excited state of special FMO
! <== case DYNAMIC = intial MO for < ELECTRON > wavepacket in DONOR fragment
LCMO = ! <== .TRUE. for initial wavepackets as Linear Combination of Molecular Orbitals (LCMO)
! <== default = .FALSE.
!--------------------------------------------------------------------
! SAMPLING parameters and SECURITY COPY
!
CT_dump_step = ! <== step for saving El&Hl survival charge density (Integer); default = 1
frame_step = ! <== step for avrg_confgs and time-slice dynamics ; frame_step =< size(trj) ; default = 1
restart = ! <== .TRUE. for restarting dynamics
step_security = ! <== step for saving backup files
! <== default = 100 (QMMM) ; 1000 (MM)
!--------------------------------------------------------------------
! DIAGNOSTIC & DATA-ANALYSIS & VISUALIZATION flags
!
HFP_Forces = ! <== .TRUE._for QMMM calcs and .FALSE. otherwise; Hellman-Feynman-Pulay forces
SPECTRUM = ! <== .TRUE. for absorption spectrum calculations
Alpha_Tensor = ! <== .TRUE. for polarizability calcs; Embeded Finite Field Polarizability
GaussianCube = ! <== .TRUE. for generating cube files for MO visualization
GaussianCube_step = ! <== time step for saving Gaussian Cube files (Integer)
DensityMatrix = ! <== .TRUE. for generating data for postprocessing with manipulate program
AutoCorrelation = ! <== .TRUE. for generating data for postprocessing with manipulate program
VDOS_ = ! <== .TRUE. velocity DOS data for postprocessing with manipulate program
!--------------------------------------------------------------------
! POTENTIALS
!
EnvField_ = ! <== .TRUE. for using electrostaic Potential produced by Environment ; default = .FALSE.
Environ_Type = ! <== choose from { Ch_MM , DP_QM , DP_MM };
! <== Ch_MM = point charges ; dipoles: { DP_QM , DP_MM } ...
! <== DP_MM = dipole moment from classical point charges
! <== DP_QM = dipole moment from quantum MO
Environ_step = ! <== step for updating EnvField (Integer) ; default = 5
Coulomb_ = ! <== .TRUE. for dipole potential for solvent molecules ; default = .FALSE.
Induced_ = ! <== .TRUE. for induced dipole potential
!--------------------------------------------------------------------
! DOS calculations
!
sigma = ! <== Gaussian broadening of DOS peaks in eV (Real) ; default = 0.04
DOS_range = real_interval( min , max ) ! <== (min,max) Real values; defines energy range of DOS calculations
!--------------------------------------------------------------------
! SPECTRUM calculations
!
occupied = real_interval( min , max ) ! <== (min,max) Real values; defines energy range of occupied MOs
empty = real_interval( min , max ) ! <== (min,max) Real values; defines energy range of empty MOs
!----------------------------------------------------------------------------------------
! MOLECULAR MECHANICS parameters
!----------------------------------------------------------------------------------------
! SYSTEM INFO
!
N_of_molecules = ! <== total number of molecules (Integer)
N_of_species = ! <== total number of species (Integer)
!------------------------------------------------------------------------------
! repeat the following information filling for all the different species ...
attention: KEEP FORMAT
!
species(1) % residue = ! <== Residue label for species 1 ; character(len3)
species(1) % N_of_molecules = ! <== Number of molecules of species (Integer)
species(1) % N_of_atoms = ! <== Number of atoms comprosing a single molecule of species i (Integer)
species(1) % flex = ! <== .TRUE. for Flexible ; .FALSE. for rigid
species(2) % residue = ! <== Residue label for species 2 ; character(len3)
species(2) % N_of_molecules = ! <== Number of molecules of species (Integer)
species(2) % N_of_atoms = ! <== Number of atoms comprosing a single molecule of species i (Integer)
species(2) % flex = ! <== .TRUE. for Flexible ; .FALSE. for rigid
.
.
.
.
species(n) % residue = ! <== Residue label for species n ; character(len3)
species(n) % N_of_molecules = ! <== Number of molecules of species (Integer)
species(n) % N_of_atoms = ! <== Number of atoms comprosing a single molecule of species i (Integer)
species(n) % flex = ! <== .TRUE. for Flexible ; .FALSE. for rigid
Selective_Dynamics = ! <== .TRUE. for ad_hoc_MM_tuning of MegaMass to selected atoms ; default = .FALSE.
!------------------------------------------------------------------------------
! AD-HOC settings
! (ad_hoc = true)
ad_hoc:QM_MM:feature(start:end) = fixing ! <== QM_MM = QM or MM (apply settings to either realm)
ad_hoc:QM_MM:feature(start:end) = fixing ! <== feature = {residue , nr , fragment , V_shift , etc ...}; check types
ad_hoc:QM_MM:feature(start:end) = fixing ! <== (start:end) range of change, end >= start; atom index
. ! <== fixing, depends on feature: 3-letter label, int_value, or real_value
.
!------------------------------------------------------------------------------
! ENVIRONMENT parameters
!
thermostat = ! <== choose from { Berendsen, Nose_Hoover, Microcanonical }
temperature = ! <== Bath Temperature (K) , (Real) ; default = 300
pressure = ! <== Pressure in atm , (Real) ; default = 1
thermal_relaxation_time = ! <== Temperature coupling term with the bath (Real)
! <== SMALL = STRONG coupling ; use "infty" to decouple
! <== picosecond ; default 0.25
pressure_relaxation_time = ! <== Pressure coupling term (Real)
! <== SMALL = STRONG coupling ; use "infty" to decouple
! <== picosecond ; default = infty
cutoff_radius = ! <== Cut off radius (Angs.) for electrostatic and LJ interactions (Real) ; default = 50.
damping_Wolf = ! <== damping parameter (Angs.^-1) ; default value = 0.001
! <== Wolf's method damping parameter (length^{-1}) ; (J. Chem. Phys. 1999; 110(17):8254)
! <== relevant quantity: R_c*Wolf ~ ....
!------------------------------------------------------------------------------
! EXECUTION INFO
!
driver_MM = ! <== choose from { MM_Dynamics , MM_Optimize , NormalModes , Parametrize }
read_velocities = ! <== .TRUE. for reading the initial velocities : T_ , F_ ; default = .TRUE.
MM_input_format = ! <== choose from { GMX, NAMD, GAFF } ; GMX = OPLS , GAFF and NAMD = Amber
MM_log_step = ! <== step for saving MM results & parameters (Integer) ; default = 50
MM_frame_step = ! <== step for saving MM results & parameters (Integer) ; default = 50
Units_MM = ! <== choose OUTPUT energy units: eV or kj-mol ; default = eV
!------------------------------------------------------------------------------
! Genetic_Alg and CG OPTIMIZATION parameters
!
Pop_Size = Integer ! <== Population size of candidate solutions for Genetic-Algorithm (Integer)
N_generations = Integer ! <== number of iterations (Integer)
Pop_range = Real ! <== range of variation of parameters [0:1] (Real)
selection_by = ! <== option = {roullete,ranking,sorting}; fitness selection method
Mutation_rate = Real ! <== range of variation of parameters [0:1] (Real)
Adaptive_ = Logical ! <== true -> Adaptive GA method; gradually tightens cost function on-the-fly (Logical)
Mutate_Cross = Logical ! <== false -> pure Genetic Algorithm ; prefer false for fine tunning! (Logical)
CG_ = Logical ! <== for using CONJUGATE GRADIENT method on Top_Selection after genetic algorithm (Logical)
Top_Selection = Integer ! <== top selection to undergo CG_
profiling = Logical ! <== generates analysis of the optimization process