A module to read and handle chemical systems. More...

Data Types
type	estruct_type
	Electronic structure type. More...

type	system_type
	System type. More...

Functions/Subroutines
subroutine, public	prg_get_nameandext (fullfilename, filename, ext)
	Get the name and extension of a file. More...

subroutine, public	prg_parse_system (system, filename, extin)
	The parser for the chemical system. More...

subroutine, public	prg_destroy_system (sy)
	Deallocates all the arrays within a system. More...

subroutine, public	prg_destroy_estr (estr)
	Deallocates all the arrays within the electronic structure. More...

subroutine, public	prg_write_system (system, filename, extin)
	Write system in .xyz, .dat or pdb file. More...

subroutine, public	prg_write_trajectory (system, iter, each, prg_deltat, filename, extension)
	Write trajectory in .xyz, .dat or pdb file. More...

subroutine, public	prg_write_trajectoryandproperty (system, iter, each, prg_deltat, scalarprop, filename, extension)
	Write trajectory and atomic properties. Only pdb file. More...

subroutine, public	prg_make_random_system (system, nats, seed, lx, ly, lz)
	Make random Xx system. More...

subroutine, public	prg_parameters_to_vectors (abc_angles, lattice_vector)
	Transforms the lattice parameters into lattice vectors. More...

subroutine, public	prg_vectors_to_parameters (lattice_vector, abc_angles)
	Transforms the lattice vectors into lattice parameters. More...

subroutine, public	prg_get_origin (coords, origin)
	Get the origin of the coordinates. More...

subroutine, public	prg_get_distancematrix (coords, dmat)
	Get the distance matrix. More...

subroutine, public	prg_translateandfoldtobox (coords, lattice_vectors, origin, verbose)
	Translate and fold to box. More...

subroutine, public	prg_centeratbox (coords, lattice_vectors, verbose)
	Translate geometric center to the center of the box. More...

subroutine, public	prg_wraparound (coords, lattice_vectors, index, verbose)
	Wrap around atom i using pbc. More...

subroutine, public	prg_translatetogeomcandfoldtobox (coords, lattice_vectors, origin)
	Translate to geometric center. More...

subroutine, public	prg_replicate (coords, symbols, lattice_vectors, nx, ny, nz)
	Extend/replicate system along lattice vectors. More...

subroutine, public	prg_replicate_system (sy, syf, nx, ny, nz)
	Extend/replicate a system type along the lattice vectors. More...

subroutine, public	prg_cleanuprepeatedatoms (nats, coords, symbols, verbose)
	Cleanup repeated atoms we might have in the system. More...

subroutine, public	prg_get_recip_vects (lattice_vectors, recip_vectors, volr, volk)
	Get the volume of the cell and the reciprocal vectors: This soubroutine computes: More...

subroutine, public	prg_get_dihedral (coords, id1, id2, id3, id4, dihedral)
	Get the dihedral angle given four atomic positions. More...

subroutine, public	prg_get_covgraph (sy, nnStruct, nrnnstruct, bml_type, factor, gcov_bml, mdimin, verbose)
	Get the covalency graph in bml format. More...

subroutine	prg_get_covgraph_int (sy, nnStructMindist, nnStruct, nrnnstruct, bml_type, factor, gcov_bml, mdimin, verbose)

subroutine, public	prg_get_covgraph_h (sy, nnStruct, nrnnstruct, rcut, graph_h, mdimin, verbose)
	Get the covanlency graph. More...

subroutine, public	prg_get_subsystem (sy, lsize, indices, sbsy, verbose)
	Get a subsystem out of the total system. More...

subroutine, public	prg_destroy_subsystems (sbsy, verbose)
	Destroy allocated subsystem. More...

subroutine, public	prg_molpartition (sy, npart, nnStructMindist, nnStruct, nrnnstruct, hetatm, gp, verbose)
	Partition by molecule. More...

subroutine, public	prg_get_partial_atomgraph (rho_bml, hindex, gch_bml, threshold, verbose)
	Get partial subgraph based on the Density matrix. More...

subroutine, public	prg_collect_graph_p (rho_bml, nc, nats, hindex, chindex, graph_p, threshold, mdimin, verbose)
	Collect the small graph to build the full graph. More...

subroutine, public	prg_merge_graph (graph_p, graph_h)
	Get partial subgraph based on the Density matrix. More...

subroutine, public	prg_merge_graph_adj (graph_p, graph_h, xadj, adjncy)
	Get partial subgraph based on the Density matrix. More...

subroutine, public	prg_adj2bml (xadj, adjncy, bml_type, g_bml)
	prg_adj2bml More...

subroutine, public	prg_graph2bml (graph, bml_type, g_bml)
	Graph2bml. More...

subroutine, public	prg_graph2vector (graph, vector, maxnz)
	Vectorize graph. More...

subroutine, public	prg_vector2graph (vector, graph, maxnz)
	Back to graph. More...

subroutine, public	prg_sortadj (xadj, adjncy)
	Sort adj NOTE: this might not be needed anymre since the bml_get_adj routine is sorting the values. More...

Variables
integer, parameter	dp = kind(1.0d0)

Detailed Description

A module to read and handle chemical systems.

This module will be used to build and handle a molecular system.

Function/Subroutine Documentation

◆ prg_adj2bml()

subroutine, public prg_system_mod::prg_adj2bml	(	integer, dimension(:), intent(in)	xadj,
		integer, dimension(:), intent(in)	adjncy,
		character(20), intent(in)	bml_type,
		type(bml_matrix_t), intent(inout)	g_bml
	)

prg_adj2bml

Parameters

xadj	CSR start values for the adjacency matrix.
adjncy	CSR positions of adjacency matrix.
bml_type	bml format.
g_bml	graph in bml format.

Definition at line 2612 of file prg_system_mod.F90.

◆ prg_centeratbox()

subroutine, public prg_system_mod::prg_centeratbox	(	real(dp), dimension(:,:), intent(inout), allocatable	coords,
		real(dp), dimension(:,:), intent(in)	lattice_vectors,
		integer, intent(in), optional	verbose
	)

Translate geometric center to the center of the box.

Parameters

coords	Coordinates of the system (see system_type).
lattice_vectors	System lattice vectors.
verbose	Verbosity level.

Definition at line 1417 of file prg_system_mod.F90.

◆ prg_cleanuprepeatedatoms()

subroutine, public prg_system_mod::prg_cleanuprepeatedatoms	(	integer, intent(inout)	nats,
		real(dp), dimension(:,:), intent(inout), allocatable	coords,
		character(len=*), dimension(:), intent(inout), allocatable	symbols,
		integer, intent(in), optional	verbose
	)

Cleanup repeated atoms we might have in the system.

Parameters

nats	Number of atoms in the system.
coords	Coordinates of the system (see system_type).
symbols	Atomic symbols (see system_type). \verbose Verbosity level.

Definition at line 1697 of file prg_system_mod.F90.

◆ prg_collect_graph_p()

subroutine, public prg_system_mod::prg_collect_graph_p	(	type(bml_matrix_t), intent(in)	rho_bml,
		integer, intent(in)	nc,
		integer, intent(in)	nats,
		integer, dimension(:,:), intent(in)	hindex,
		integer, dimension(:), intent(in)	chindex,
		integer, dimension(:,:), intent(inout), allocatable	graph_p,
		real(dp), intent(in)	threshold,
		integer, intent(in)	mdimin,
		integer, intent(in), optional	verbose
	)

Collect the small graph to build the full graph.

Parameters

rho_bml	Density matix in bml format.
nc	Number of core atoms.
nats	Number of atoms.
hindex	Hindex for the small part (see haindex)
chindex	Core-hallo index for the small part.
graph_p	Graph in an "ellpack" format.
threshold	Threshold to buil the density based atom projected graph.
verbose	Verbosity level.

Definition at line 2395 of file prg_system_mod.F90.

◆ prg_destroy_estr()

subroutine, public prg_system_mod::prg_destroy_estr ( type(estruct_type), intent(inout) estr )

Deallocates all the arrays within the electronic structure.

Parameters

estr	Electronic Structure type

Definition at line 704 of file prg_system_mod.F90.

◆ prg_destroy_subsystems()

subroutine, public prg_system_mod::prg_destroy_subsystems	(	type(system_type), intent(inout)	sbsy,
		integer, intent(in), optional	verbose
	)

Destroy allocated subsystem.

This routine will deallocate all the arrays of the structures.

Parameters

sy	System to de deallocated (see system_type).

Definition at line 2176 of file prg_system_mod.F90.

◆ prg_destroy_system()

subroutine, public prg_system_mod::prg_destroy_system ( type(system_type), intent(inout) sy )

Deallocates all the arrays within a system.

Parameters

sy	System type

Definition at line 677 of file prg_system_mod.F90.

◆ prg_get_covgraph()

subroutine, public prg_system_mod::prg_get_covgraph	(	type(system_type), intent(in)	sy,
		integer, dimension(:,:), intent(in)	nnStruct,
		integer, dimension(:), intent(in)	nrnnstruct,
		character(20), intent(in)	bml_type,
		real(dp)	factor,
		type(bml_matrix_t), intent(inout)	gcov_bml,
		integer, intent(in)	mdimin,
		integer, intent(in), optional	verbose
	)

Get the covalency graph in bml format.

This is the graph composed by the covalent bonds (edges) that are determined with the VDW radius.

Parameters

sy	System structure (see system_type).
nnStruct	The neigbors J to I within Rcut that are all within the box.
nrnnstruct	Number of neigbors to I within Rcut that are all within the box.
bml_type	The bml type for constructing the graph.
gconv_bml	Covanlency graph in bml format.
verbose	Verbosity level.

Definition at line 1882 of file prg_system_mod.F90.

◆ prg_get_covgraph_h()

subroutine, public prg_system_mod::prg_get_covgraph_h	(	type(system_type), intent(in)	sy,
		integer, dimension(:,:), intent(in)	nnStruct,
		integer, dimension(:), intent(in)	nrnnstruct,
		real(dp), intent(in)	rcut,
		integer, dimension(:,:), intent(inout), allocatable	graph_h,
		integer, intent(in)	mdimin,
		integer, intent(in), optional	verbose
	)

Get the covanlency graph.

This is the graph composed by the covalent bonds (edges) that are determined with the VDW radius.

Parameters

sy	System structure (see system_type).
nnStruct	The neigbors J to I within Rcut that are all within the box.
nrnnstruct	Number of neigbors to I within Rcut that are all within the box.
bml_type	The bml type for constructing the graph.
gconv_bml	Covanlency graph in bml format.
verbose	Verbosity level.

Definition at line 2017 of file prg_system_mod.F90.

◆ prg_get_covgraph_int()

subroutine prg_system_mod::prg_get_covgraph_int	(	type(system_type), intent(in)	sy,
		real(dp), dimension(:,:), intent(in)	nnStructMindist,
		integer, dimension(:,:), intent(in)	nnStruct,
		integer, dimension(:), intent(in)	nrnnstruct,
		character(20), intent(in)	bml_type,
		real(dp)	factor,
		type(bml_matrix_t), intent(inout)	gcov_bml,
		integer, intent(in)	mdimin,
		integer, intent(in), optional	verbose
	)

private

Definition at line 1958 of file prg_system_mod.F90.

◆ prg_get_dihedral()

subroutine, public prg_system_mod::prg_get_dihedral	(	real(dp), dimension(:,:), intent(in)	coords,
		integer, intent(in)	id1,
		integer, intent(in)	id2,
		integer, intent(in)	id3,
		integer, intent(in)	id4,
		real(dp), intent(out)	dihedral
	)

Get the dihedral angle given four atomic positions.

Parameters

sy	System structure
id1	Atom index 1
id2	Atom index 1
id3	Atom index 1
id4	Atom index 1
dihedral	Output dihedral angle

Definition at line 1827 of file prg_system_mod.F90.

◆ prg_get_distancematrix()

subroutine, public prg_system_mod::prg_get_distancematrix	(	real(dp), dimension(:,:), intent(in)	coords,
		real(dp), dimension(:,:), intent(out), allocatable	dmat
	)

Get the distance matrix.

Parameters

coords	Coordinates of the system (see system_type).
dmat	Distance matrix (nats x nats).

Definition at line 1339 of file prg_system_mod.F90.

◆ prg_get_nameandext()

subroutine, public prg_system_mod::prg_get_nameandext	(	character(len=*), intent(in)	fullfilename,
		character(50), intent(inout)	filename,
		character(3), intent(inout)	ext
	)

Get the name and extension of a file.

Parameters

fullfilename	Full filename.
filename	Filename of the system.
extension	Extension of the file.

Definition at line 244 of file prg_system_mod.F90.

◆ prg_get_origin()

subroutine, public prg_system_mod::prg_get_origin	(	real(dp), dimension(:,:), intent(in)	coords,
		real(dp), dimension(:), intent(inout), allocatable	origin
	)

Get the origin of the coordinates.

Parameters

coords	Coordinates of teh system (see system_type).
origin	(min(x),min(y),min(z)) set as the origin of the system.

Definition at line 1306 of file prg_system_mod.F90.

◆ prg_get_partial_atomgraph()

subroutine, public prg_system_mod::prg_get_partial_atomgraph	(	type(bml_matrix_t), intent(in)	rho_bml,
		integer, dimension(:,:), intent(in)	hindex,
		type(bml_matrix_t), intent(inout)	gch_bml,
		real(dp), intent(in)	threshold,
		integer, intent(in), optional	verbose
	)

Get partial subgraph based on the Density matrix.

Parameters

rho_bml	Density matix in bml format.
hindex	Start and end index for every atom in the system.
gch_bml	Atom based graph in bml format.
threshold	Threshold value for constructing the graph.
verbose	Verbosity levels.

Definition at line 2329 of file prg_system_mod.F90.

◆ prg_get_recip_vects()

subroutine, public prg_system_mod::prg_get_recip_vects	(	real(dp), dimension(:,:), intent(in)	lattice_vectors,
		real(dp), dimension(:,:), intent(inout), allocatable	recip_vectors,
		real(dp), intent(inout)	volr,
		real(dp), intent(inout)	volk
	)

Get the volume of the cell and the reciprocal vectors: This soubroutine computes:

\( b_1 = \frac{1}{V_c} a_1 \times a_2 \)
\( b_2 = \frac{1}{V_c} a_2 \times a_3 \)
\( b_3 = \frac{1}{V_c} a_3 \times a_1 \)
\( V_c = || a_1\cdot (a_2 \times a_3)||\)
\( V_{BZ} = || b_1\cdot (b_2 \times b_3)||\)
Parameters

lattice_vectors Lattice vectors for the system.

recip_vectors Reciprocal vectors of the system.

volr Volume of the cell.

volk Volume of the reciprocal cell.

Definition at line 1778 of file prg_system_mod.F90.

◆ prg_get_subsystem()

subroutine, public prg_system_mod::prg_get_subsystem	(	type(system_type), intent(in)	sy,
		integer, intent(in)	lsize,
		integer, dimension(:), intent(in)	indices,
		type(system_type), intent(inout)	sbsy,
		integer, intent(in), optional	verbose
	)

Get a subsystem out of the total system.

This will get a subsystem from the total system guided by a partition.

Parameters

sy	System structure (see system_type).
lsize	Core+Hallo subsystem size.
indices	Partition indices.
sbsy	Subsystem to be extracted.

Definition at line 2087 of file prg_system_mod.F90.

◆ prg_graph2bml()

subroutine, public prg_system_mod::prg_graph2bml	(	integer, dimension(:,:), intent(inout), allocatable	graph,
		character(20), intent(in)	bml_type,
		type(bml_matrix_t), intent(inout)	g_bml
	)

Graph2bml.

Parameters

graph	Atom based graph in "ellpack" like format.
bml_type	Bml type (usually ellpack for graph starage)
g_bml	Graph in bml format.

Definition at line 2646 of file prg_system_mod.F90.

◆ prg_graph2vector()

subroutine, public prg_system_mod::prg_graph2vector	(	integer, dimension(:,:), intent(inout)	graph,
		integer, dimension(:), allocatable	vector,
		integer	maxnz
	)

Vectorize graph.

Parameters

graph	Ellpack graph.
vector	Vector to store the graph.

Definition at line 2689 of file prg_system_mod.F90.

◆ prg_make_random_system()

subroutine, public prg_system_mod::prg_make_random_system	(	type(system_type), intent(out)	system,
		integer	nats,
		integer	seed,
		real(dp)	lx,
		real(dp)	ly,
		real(dp)	lz
	)

Make random Xx system.

Parameters

system	System to be construucted.
nats	Number of atoms.
lx	length of the box for the x coordinate.
ly	length of the box for the y coordinate.
lz	length of the box for the z coordinate.

Definition at line 1182 of file prg_system_mod.F90.

◆ prg_merge_graph()

subroutine, public prg_system_mod::prg_merge_graph	(	integer, dimension(:,:), intent(inout)	graph_p,
		integer, dimension(:,:), intent(inout)	graph_h
	)

Get partial subgraph based on the Density matrix.

Parameters

graph_p	Density matix based graph in bml format.
graph_h	Hamiltonian matix based graph in bml format.

Definition at line 2487 of file prg_system_mod.F90.

◆ prg_merge_graph_adj()

subroutine, public prg_system_mod::prg_merge_graph_adj	(	integer, dimension(:,:), intent(inout), allocatable	graph_p,
		integer, dimension(:,:), intent(inout), allocatable	graph_h,
		integer, dimension(:), intent(inout), allocatable	xadj,
		integer, dimension(:), intent(inout), allocatable	adjncy
	)

Get partial subgraph based on the Density matrix.

Parameters

graph_p	Density matix based graph in "ellpack type format".
graph_h	Hamiltonian matix based graph in "ellpack type format".
xadj	CSR start values for the adjacency matrix.
adjncy	CSR positions of adjacency matrix.

Definition at line 2538 of file prg_system_mod.F90.

◆ prg_molpartition()

subroutine, public prg_system_mod::prg_molpartition	(	type(system_type), intent(in)	sy,
		integer, intent(inout)	npart,
		real(dp), dimension(:,:), intent(in)	nnStructMindist,
		integer, dimension(:,:), intent(in)	nnStruct,
		integer, dimension(:), intent(in)	nrnnstruct,
		character(2), intent(in)	hetatm,
		type(graph_partitioning_t), intent(inout)	gp,
		integer, intent(inout), optional	verbose
	)

Partition by molecule.

Parameters

sy	System structure.
npart	Number of parts.
nnStructMindist	Minimum distance between neighbors.
nnStruct	The neighbors J to I within Rcut that are all within the box.
nrnnstruct	Number of neighbors to I within Rcut that are all within the box.
hetatm	Atom to be taken as the "center" of the by molecule partition.
gp	Graph partition structure.
verbose	Verbosity level.

Definition at line 2240 of file prg_system_mod.F90.

◆ prg_parameters_to_vectors()

subroutine, public prg_system_mod::prg_parameters_to_vectors	(	real(dp), dimension(2,3), intent(in)	abc_angles,
		real(dp), dimension(3,3), intent(out)	lattice_vector
	)

Transforms the lattice parameters into lattice vectors.

Parameters

abc_angles	2x3 array containing the lattice parameters. abc_angles(1,1) = a, abc_angles(1,2) = b, and abc_angles(1,3) = c abc_angles(2,1) = \( \alpha \) , abc_angles(2,2) = \( \beta \) and abc_angles(2,3) = \( \gamma \)
lattice_vector	3x3 array containing the lattice vectors. lattice_vector(1,:) = \( \overrightarrow{a} \)

Definition at line 1228 of file prg_system_mod.F90.

◆ prg_parse_system()

subroutine, public prg_system_mod::prg_parse_system	(	type(system_type), intent(out)	system,
		character(len=*)	filename,
		character(3), intent(in), optional	extin
	)

The parser for the chemical system.

Parameters

system	System to be constructed.
filename	Filename of the system.
extin	Extension of the file.

Assignment of species index for every atom.

Todo:: Integrate this loop in the loop for building the splist.

Definition at line 267 of file prg_system_mod.F90.

◆ prg_replicate()

subroutine, public prg_system_mod::prg_replicate	(	real(dp), dimension(:,:), intent(inout), allocatable	coords,
		character(2), dimension(:), intent(inout), allocatable	symbols,
		real(dp), dimension(:,:), intent(inout)	lattice_vectors,
		integer, intent(in)	nx,
		integer, intent(in)	ny,
		integer, intent(in)	nz
	)

Extend/replicate system along lattice vectors.

Parameters

coords	Coordinates of the system (see system_type).
symbols	Symbols for elements.
lattice_vectors	System lattice vectors.
nx	Number of lattice points in the v1 direction.
ny	Number of lattice points in the v2 direction.
nz	Number of lattice points in the v2 direction.

Definition at line 1543 of file prg_system_mod.F90.

◆ prg_replicate_system()

subroutine, public prg_system_mod::prg_replicate_system	(	type(system_type), intent(inout)	sy,
		type(system_type)	syf,
		integer, intent(in)	nx,
		integer, intent(in)	ny,
		integer, intent(in)	nz
	)

Extend/replicate a system type along the lattice vectors.

Parameters

sy	System type.
syf	System type output.
nx	Number of lattice points in the v1 direction.
ny	Number of lattice points in the v2 direction.
nz	Number of lattice points in the v2 direction.

Definition at line 1600 of file prg_system_mod.F90.

◆ prg_sortadj()

subroutine, public prg_system_mod::prg_sortadj	(	integer, dimension(:), intent(inout)	xadj,
		integer, dimension(:), intent(inout), allocatable	adjncy
	)

Sort adj NOTE: this might not be needed anymre since the bml_get_adj routine is sorting the values.

Definition at line 2746 of file prg_system_mod.F90.

◆ prg_translateandfoldtobox()

subroutine, public prg_system_mod::prg_translateandfoldtobox	(	real(dp), dimension(:,:), intent(inout), allocatable	coords,
		real(dp), dimension(:,:), intent(in)	lattice_vectors,
		real(dp), dimension(:), intent(inout), allocatable	origin,
		integer, intent(in), optional	verbose
	)

Translate and fold to box.

Parameters

coords	Coordinates of the system (see system_type).
lattice_vectors	System lattice vectors.
origin	(min(x),min(y),min(z)) set as the origin of the system.

Definition at line 1364 of file prg_system_mod.F90.

◆ prg_translatetogeomcandfoldtobox()

subroutine, public prg_system_mod::prg_translatetogeomcandfoldtobox	(	real(dp), dimension(:,:), intent(inout), allocatable	coords,
		real(dp), dimension(:,:), intent(in)	lattice_vectors,
		real(dp), dimension(:), intent(inout), allocatable	origin
	)

Translate to geometric center.

Parameters

coords	Coordinates of the system (see system_type).
lattice_vectors	System lattice vectors.
origin	(min(x),min(y),min(z)) set as the origin of the system.

Definition at line 1504 of file prg_system_mod.F90.

◆ prg_vector2graph()

subroutine, public prg_system_mod::prg_vector2graph	(	integer, dimension(:), intent(inout), allocatable	vector,
		integer, dimension(:,:), intent(inout)	graph,
		integer	maxnz
	)

Back to graph.

Parameters

vector	Vector to store the graph.
graph	Ellpack graph.

Definition at line 2718 of file prg_system_mod.F90.

◆ prg_vectors_to_parameters()

subroutine, public prg_system_mod::prg_vectors_to_parameters	(	real(dp), dimension(3,3), intent(in)	lattice_vector,
		real(dp), dimension(2,3), intent(out)	abc_angles
	)

Transforms the lattice vectors into lattice parameters.

Parameters

lattice_vector	3x3 array containing the lattice vectors. lattice_vector(1,:) = \( \overrightarrow{a} \)
abc_angles	2x3 array containing the lattice parameters. abc_angles(1,1) = a, abc_angles(1,2) = b and abc_angles(1,3) = c abc_angles(2,1) = \( \alpha \), abc_angles(2,2) = \( \beta \), and abc_angles(2,3) = \( \gamma \).

Definition at line 1270 of file prg_system_mod.F90.

◆ prg_wraparound()

subroutine, public prg_system_mod::prg_wraparound	(	real(dp), dimension(:,:), intent(inout), allocatable	coords,
		real(dp), dimension(:,:), intent(in)	lattice_vectors,
		integer, intent(in)	index,
		integer, intent(in), optional	verbose
	)

Wrap around atom i using pbc.

Parameters

coords	Coordinates of the system (see system_type).
lattice_vectors	System lattice vectors.
index	Index atom to wrap around

Definition at line 1459 of file prg_system_mod.F90.

◆ prg_write_system()

subroutine, public prg_system_mod::prg_write_system	(	type(system_type), intent(inout)	system,
		character(len=*)	filename,
		character(3), intent(in), optional	extin
	)

Write system in .xyz, .dat or pdb file.

Parameters

system	System to be constructed.
filename	File name.
extension	Extension of the file.

Definition at line 737 of file prg_system_mod.F90.

◆ prg_write_trajectory()

subroutine, public prg_system_mod::prg_write_trajectory	(	type(system_type), intent(in)	system,
		integer, intent(in)	iter,
		integer, intent(in)	each,
		real(dp), intent(in)	prg_deltat,
		character(len=*)	filename,
		character(3)	extension
	)

Write trajectory in .xyz, .dat or pdb file.

Parameters

system	System to be appended to the trajectory file.
iter	Simulation step.
each	Writing frequency.
filename	File name for the trajectory.
extension	Extension of the file.

Definition at line 949 of file prg_system_mod.F90.

◆ prg_write_trajectoryandproperty()

subroutine, public prg_system_mod::prg_write_trajectoryandproperty	(	type(system_type), intent(in)	system,
		integer, intent(in)	iter,
		integer, intent(in)	each,
		real(dp), intent(in)	prg_deltat,
		real(dp), dimension(:), intent(in)	scalarprop,
		character(len=*)	filename,
		character(3)	extension
	)

Write trajectory and atomic properties. Only pdb file.

Parameters

system	System to be appended to the trajectory file.
iter	Simulation step.
each	Writing frequency.
prg_deltat	Integration step.
scalarprop	Scalar property to plot on atoms.
filename	File name for the trajectory.
extension	Extension of the file.

Definition at line 1072 of file prg_system_mod.F90.

Variable Documentation

◆ dp

integer, parameter prg_system_mod::dp = kind(1.0d0)

private

Definition at line 17 of file prg_system_mod.F90.

lattice_vectors	Lattice vectors for the system.
recip_vectors	Reciprocal vectors of the system.
volr	Volume of the cell.
volk	Volume of the reciprocal cell.

Data Types

Functions/Subroutines

Variables

Detailed Description

Function/Subroutine Documentation

◆ prg_adj2bml()

◆ prg_centeratbox()

◆ prg_cleanuprepeatedatoms()

◆ prg_collect_graph_p()

◆ prg_destroy_estr()

◆ prg_destroy_subsystems()

◆ prg_destroy_system()

◆ prg_get_covgraph()

◆ prg_get_covgraph_h()

◆ prg_get_covgraph_int()

◆ prg_get_dihedral()

◆ prg_get_distancematrix()

◆ prg_get_nameandext()

◆ prg_get_origin()

◆ prg_get_partial_atomgraph()

◆ prg_get_recip_vects()

◆ prg_get_subsystem()

◆ prg_graph2bml()

◆ prg_graph2vector()

◆ prg_make_random_system()

◆ prg_merge_graph()

◆ prg_merge_graph_adj()

◆ prg_molpartition()

◆ prg_parameters_to_vectors()

◆ prg_parse_system()

◆ prg_replicate()

◆ prg_replicate_system()

◆ prg_sortadj()

◆ prg_translateandfoldtobox()

◆ prg_translatetogeomcandfoldtobox()

◆ prg_vector2graph()

◆ prg_vectors_to_parameters()

◆ prg_wraparound()

◆ prg_write_system()

◆ prg_write_trajectory()

◆ prg_write_trajectoryandproperty()

Variable Documentation

◆ dp