contains miscellaneous subroutines used in the Monte Carlo runs,mostly geared towards changes in coordinates More...
Functions | |
| subroutine, public | check_for_overlap (force_env, nchains, nunits, loverlap, mol_type, cell_length, molecule_number) |
| looks for overlaps (intermolecular distances less than rmin) | |
| subroutine, public | get_center_of_mass (coordinates, natom, center_of_mass, mass) |
| calculates the center of mass of a given molecule | |
| subroutine, public | mc_coordinate_fold (coordinates, nchains_tot, mol_type, mass, nunits, box_length) |
| folds all the coordinates into the center simulation box using a center of mass cutoff | |
| subroutine, public | generate_cbmc_swap_config (force_env, BETA, max_val, min_val, exp_max_val, exp_min_val, nswapmoves, rosenbluth_weight, start_atom, natoms_tot, nunits, nunits_mol, mass, loverlap, choosen_energy, old_energy, ionode, lremove, mol_type, nchains, source, group, rng_stream, error, avbmc_atom, rmin, rmax, move_type, target_atom) |
| takes the last molecule in a force environment and moves it around to different center of mass positions and orientations, selecting one based on the rosenbluth weight | |
| subroutine, public | rotate_molecule (r, mass, natoms, rng_stream, error) |
| rotates a molecule randomly around the center of mass, sequentially in x, y, and z directions | |
| subroutine, public | find_mc_test_molecule (mc_molecule_info, start_atom, box_number, molecule_type, rng_stream, box, molecule_type_old, error) |
| selects a molecule at random to perform a MC move on...you can specify the box the molecule should be in, its type, both, or neither | |
| subroutine, public | create_discrete_array (cell, discrete_array, step_size) |
| generates an array that tells us which sides of the simulation cell we can increase or decrease using a discrete volume move | |
| subroutine, private | generate_avbmc_insertion (rmin, rmax, r_target, move_type, r_insert, abc, rng_stream, error) |
| generates an insertion point in either the "in" or the "out" volume of a target atom, where the "in" volume is a shell with inner radius rmin and outer radius rmax | |
Variables | |
| CHARACTER(len=*), parameter, private | moduleN = 'mc_coordinates' |
Detailed Description
contains miscellaneous subroutines used in the Monte Carlo runs,mostly geared towards changes in coordinates
Function Documentation
| subroutine,public mc_coordinates::check_for_overlap | ( | TYPE(force_env_type),pointer | force_env, |
| INTEGER,dimension(:),intent(in) | nchains, | ||
| INTEGER,dimension(:),intent(in) | nunits, | ||
| LOGICAL,intent(out) | loverlap, | ||
| INTEGER,dimension(:),intent(in) | mol_type, | ||
| REAL(KIND=dp),dimension(1:3),intent(in),optional | cell_length, | ||
| INTEGER,intent(in),optional | molecule_number | ||
| ) |
looks for overlaps (intermolecular distances less than rmin)
- Parameters:
-
force_env the force environment containing the coordinates nchains the number of molecules of each type in the box nunits the number of interaction sites for each molecule loverlap returns .TRUE. if atoms overlap mol_type an array that indicates the type of each molecule cell_length the length of the box...if none is specified, it uses the cell found in the force_env molecule_number if present, just look for overlaps with this molecule
Suitable for parallel use.
Definition at line 69 of file mc_coordinates.f90.
References cp_subsys_types::cp_subsys_get(), force_env_types::force_env_get(), and timings::timeset().
Referenced by generate_cbmc_swap_config(), mc_ensembles::mc_compute_virial(), mc_moves::mc_conformation_change(), mc_ge_moves::mc_ge_swap_move(), mc_ge_moves::mc_ge_volume_move(), mc_moves::mc_molecule_rotation(), mc_moves::mc_molecule_translation(), mc_ge_moves::mc_Quickstep_move(), mc_ensembles::mc_run_ensemble(), and mc_moves::mc_volume_move().
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| subroutine,public mc_coordinates::create_discrete_array | ( | REAL(dp),dimension(1:3),intent(in) | cell, |
| INTEGER,dimension(1:3, 1:2),intent(out) | discrete_array, | ||
| REAL(dp),intent(in) | step_size | ||
| ) |
generates an array that tells us which sides of the simulation cell we can increase or decrease using a discrete volume move
- Parameters:
-
cell the lengths of the sides of the cell discrete_array the array that indicates which sides we can move step_size the size of the discrete volume move
Suitable for parallel.
Definition at line 931 of file mc_coordinates.f90.
| subroutine,public mc_coordinates::find_mc_test_molecule | ( | TYPE(mc_molecule_info_type),pointer | mc_molecule_info, |
| INTEGER,intent(out) | start_atom, | ||
| INTEGER,intent(out) | box_number, | ||
| INTEGER,intent(out) | molecule_type, | ||
| TYPE(rng_stream_type),pointer | rng_stream, | ||
| INTEGER,intent(in),optional | box, | ||
| INTEGER,intent(in),optional | molecule_type_old, | ||
| TYPE(cp_error_type),intent(inout) | error | ||
| ) |
selects a molecule at random to perform a MC move on...you can specify the box the molecule should be in, its type, both, or neither
- Parameters:
-
mc_molecule_info the structure that contains some global molecule data start_atom the number of the first atom in the choosen molecule in relation to the force_env it's in box_number the box the choosen molecule is in molecule_type the type of molecule the choosen molecule is rng_stream the stream we pull random numbers from box if present, tells the routine which box to grab a molecule from molecule_type_old if present, tells the routine which molecule type to select from error the optional cp_error_type
Designed only for serial use.
Definition at line 774 of file mc_coordinates.f90.
References CPPostcondition, error, mc_types::get_mc_molecule_info(), and timings::timeset().
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| subroutine,private mc_coordinates::generate_avbmc_insertion | ( | REAL(KIND=dp),intent(in) | rmin, |
| REAL(KIND=dp),intent(in) | rmax, | ||
| REAL(KIND=dp),dimension(1:3),intent(in) | r_target, | ||
| CHARACTER(LEN=*),intent(in) | move_type, | ||
| REAL(KIND=dp),dimension(1:3),intent(out) | r_insert, | ||
| REAL(KIND=dp),dimension(1:3),intent(in) | abc, | ||
| TYPE(rng_stream_type),pointer | rng_stream, | ||
| TYPE(cp_error_type),intent(inout) | error | ||
| ) | [private] |
generates an insertion point in either the "in" or the "out" volume of a target atom, where the "in" volume is a shell with inner radius rmin and outer radius rmax
- Parameters:
-
rmin the minimum AVBMC radius for the shell around the target rmax the maximum AVBMC radius for the shell around the target r_target the coordinates of the target atom move_type generate configs in the "in" or "out" volume r_insert the output insertion site abc the lengths of the sides of the simulation box rng_stream the random number stream that we draw from
Use only in serial.
Definition at line 997 of file mc_coordinates.f90.
References error.
Referenced by generate_cbmc_swap_config().
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| subroutine,public mc_coordinates::generate_cbmc_swap_config | ( | TYPE(force_env_type),pointer | force_env, |
| REAL(KIND=dp),intent(in) | BETA, | ||
| REAL(KIND=dp),intent(in) | max_val, | ||
| REAL(KIND=dp),intent(in) | min_val, | ||
| REAL(KIND=dp),intent(in) | exp_max_val, | ||
| REAL(KIND=dp),intent(in) | exp_min_val, | ||
| INTEGER,intent(in) | nswapmoves, | ||
| REAL(KIND=dp),intent(out) | rosenbluth_weight, | ||
| INTEGER,intent(in) | start_atom, | ||
| INTEGER,intent(in) | natoms_tot, | ||
| INTEGER,dimension(:),intent(in) | nunits, | ||
| INTEGER,intent(in) | nunits_mol, | ||
| REAL(dp),dimension(1:nunits_mol),intent(in) | mass, | ||
| LOGICAL,intent(out) | loverlap, | ||
| REAL(KIND=dp),intent(out) | choosen_energy, | ||
| REAL(KIND=dp),intent(in) | old_energy, | ||
| LOGICAL,intent(in) | ionode, | ||
| LOGICAL,intent(in) | lremove, | ||
| INTEGER,dimension(:),intent(in) | mol_type, | ||
| INTEGER,dimension(:),intent(in) | nchains, | ||
| INTEGER,intent(in) | source, | ||
| INTEGER,intent(in) | group, | ||
| TYPE(rng_stream_type),pointer | rng_stream, | ||
| TYPE(cp_error_type) | error, | ||
| INTEGER,intent(in),optional | avbmc_atom, | ||
| REAL(KIND=dp),intent(in),optional | rmin, | ||
| REAL(KIND=dp),intent(in),optional | rmax, | ||
| CHARACTER(LEN=*),intent(in),optional | move_type, | ||
| INTEGER,intent(in),optional | target_atom | ||
| ) |
takes the last molecule in a force environment and moves it around to different center of mass positions and orientations, selecting one based on the rosenbluth weight
- Optional Avbmc Flags
- avbmc_atom: the atom number that serves for the target atom in each molecule (1 is the first atom in the molecule, etc.)
- rmin: the minimum AVBMC radius for the shell around the target
- rmax: the maximum AVBMC radius for the shell around the target
- move_type: generate configs in the "in" or "out" volume
- target_atom: the number of the avbmc atom in the target molecule
- Suitable for parallel.
- Parameters:
-
force_env the force environment containing the coordinates BETA the value of 1/kT for this simulations, in a.u. nswapmoves the number of desired trial configurations rosenbluth_weight the Rosenbluth weight for this set of configs start_atom the atom number that the molecule to be swapped starts on natoms_tot the total number of interaction sites in the box nunits the number of interaction sites for every molecule_type nunits_tot the number of interaction sites in the choosen molecule mass the mass for every interaction site of every molecule type loverlap the flag that indicates if all of the configs have an atomic overlap choosen_energy the energy of the choosen config old_energy the energy that we subtract from all of the trial energies to prevent numerical overflows ionode indicates if we're on the main CPU lremove is this the Rosenbluth weight for a removal box? mol_type an array that contains the molecule type for every atom in the box nchains the number of molecules of each type in this box source the MPI source value, for broadcasts group the MPI group value, for broadcasts rng_stream the random number stream that we draw from error the the cp_error type
Definition at line 338 of file mc_coordinates.f90.
References physcon::angstrom, check_for_overlap(), cp_subsys_types::cp_subsys_get(), error, force_env_methods::force_env_calc_energy_force(), force_env_types::force_env_get(), generate_avbmc_insertion(), get_center_of_mass(), rotate_molecule(), and timings::timeset().
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| subroutine,public mc_coordinates::get_center_of_mass | ( | REAL(KIND=dp),dimension(:, :),intent(in) | coordinates, |
| INTEGER,intent(in) | natom, | ||
| REAL(KIND=dp),dimension(1:3),intent(out) | center_of_mass, | ||
| REAL(KIND=dp),dimension(:),intent(in) | mass | ||
| ) |
calculates the center of mass of a given molecule
- Parameters:
-
coordinates the coordiantes of the atoms in the molecule natom the number of atoms in the molecule center_of_mass the coordinates of the center of mass mass the mass of the atoms in the molecule
Designed for parallel use.
Definition at line 200 of file mc_coordinates.f90.
References timings::timeset().
Referenced by generate_cbmc_swap_config(), mc_coordinate_fold(), and rotate_molecule().
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| subroutine,public mc_coordinates::mc_coordinate_fold | ( | REAL(KIND=dp),dimension(:, :),intent(inout) | coordinates, |
| INTEGER,intent(in) | nchains_tot, | ||
| INTEGER,dimension(:),intent(in) | mol_type, | ||
| REAL(KIND=dp),dimension(:, :),intent(in) | mass, | ||
| INTEGER,dimension(:),intent(in) | nunits, | ||
| REAL(KIND=dp),dimension(1:3),intent(in) | box_length | ||
| ) |
folds all the coordinates into the center simulation box using a center of mass cutoff
- Parameters:
-
coordinates the coordiantes of the atoms in the system nchains_tot the total number of molecules in the box mol_type an array that indicates the type of every molecule in the box mass the mass of every atom for all molecule types nunits the number of interaction sites for each molecule type box_length an array for the lengths of the simulation box sides
Designed for parallel use.
Definition at line 250 of file mc_coordinates.f90.
References get_center_of_mass(), and timings::timeset().
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| subroutine,public mc_coordinates::rotate_molecule | ( | REAL(KIND=dp),dimension(1:3, 1:natoms),intent(inout) | r, |
| REAL(KIND=dp),dimension(1:natoms),intent(in) | mass, | ||
| INTEGER,intent(in) | natoms, | ||
| TYPE(rng_stream_type),pointer | rng_stream, | ||
| TYPE(cp_error_type),intent(inout) | error | ||
| ) |
rotates a molecule randomly around the center of mass, sequentially in x, y, and z directions
- Parameters:
-
r the coordinates of the molecule to rotate mass the mass of all the atoms in the molecule natoms the number of atoms in the molecule rng_stream the stream we pull random numbers from
Use only in serial.
Definition at line 678 of file mc_coordinates.f90.
References get_center_of_mass(), mathconstants::pi, and timings::timeset().
Referenced by generate_cbmc_swap_config().
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Variable Documentation
| CHARACTER(len=*),parameter,private mc_coordinates::moduleN = 'mc_coordinates' |
Definition at line 50 of file mc_coordinates.f90.
