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colvarproxy Class Reference

Interface class between the collective variables module and the simulation program. More...

#include <colvarproxy.h>

Inheritance diagram for colvarproxy:

colvarproxy_namd List of all members.

Public Member Functions

virtual cvm::real unit_angstrom ()=0
 Value of the unit for atomic coordinates with respect to angstroms (used by some variables for hard-coded default values).
virtual cvm::real boltzmann ()=0
 Boltzmann constant.
virtual cvm::real temperature ()=0
 Temperature of the simulation (K).
virtual void log (std::string const &message)=0
 Print a message to the main log.
virtual void fatal_error (std::string const &message)=0
 Print a message to the main log and exit with error code.
virtual void exit (std::string const &message)=0
 Print a message to the main log and exit normally.
virtual std::string input_prefix ()=0
 Prefix to be used for input files (restarts, not configuration).
virtual std::string restart_output_prefix ()=0
 Prefix to be used for output restart files.
virtual std::string output_prefix ()=0
 Prefix to be used for output files (final system configuration).
virtual size_t restart_frequency ()=0
 Restarts will be fritten each time this number of steps has passed.
virtual cvm::rvector position_distance (cvm::atom_pos const &pos1, cvm::atom_pos const &pos2)=0
 Get the simple distance vector between two positions (with periodic boundary conditions handled transparently).
virtual cvm::real position_dist2 (cvm::atom_pos const &pos1, cvm::atom_pos const &pos2)=0
 Get the square distance between two positions (with periodic boundary conditions handled transparently).
virtual void select_closest_image (cvm::atom_pos &pos, cvm::atom_pos const &ref_pos)=0
 Get the closest periodic image to a reference position.
void select_closest_images (std::vector< cvm::atom_pos > &pos, cvm::atom_pos const &ref_pos)
 Perform select_closest_image() on a set of atomic positions.
virtual void load_atoms (char const *filename, std::vector< cvm::atom > &atoms, std::string const pdb_field="O", double const pdb_field_value=0.0)
 Read atom identifiers from a file.
virtual void load_coords (char const *filename, std::vector< cvm::atom_pos > &pos, std::string const pdb_field="O", double const pdb_field_value=0.0)
 Load the coordinates for a group of atoms from a file (usually a PDB); if "pos" is already allocated, the number of its elements must match the number of atoms in "filename".
virtual void backup_file (char const *filename)
 Rename the given file, under the convention provided by the MD program.
virtual ~colvarproxy ()

Public Attributes

colvarmodule * colvars
 Pointer to the instance of colvarmodule.

Detailed Description

Interface class between the collective variables module and the simulation program.

Definition at line 12 of file colvarproxy.h.

Constructor & Destructor Documentation

virtual colvarproxy::~colvarproxy (   )  [inline, virtual]
 

Definition at line 107 of file colvarproxy.h.

00107 {}

Member Function Documentation

void colvarproxy::backup_file (  char const *  filename  )  [inline, virtual]
 

Rename the given file, under the convention provided by the MD program.

Reimplemented in colvarproxy_namd.

Definition at line 141 of file colvarproxy.h.

Referenced by colvarmodule::calc(), colvarmodule::colvarmodule(), and colvarmodule::finalise().

00142 {
00143 //   cvm::fatal_error ("Error: colvarproxy::backup_file() has not been (re)redefined, "
00144 //                     "__FILE__ at line __LINE__.\n"); 
00145 }

virtual cvm::real colvarproxy::boltzmann (   )  [pure virtual]
 

Boltzmann constant.

Implemented in colvarproxy_namd.

Referenced by colvarmodule::boltzmann().

virtual void colvarproxy::exit (  std::string const &  message  )  [pure virtual]
 

Print a message to the main log and exit normally.

Implemented in colvarproxy_namd.

Referenced by colvarmodule::exit().

virtual void colvarproxy::fatal_error (  std::string const &  message  )  [pure virtual]
 

Print a message to the main log and exit with error code.

Implemented in colvarproxy_namd.

Referenced by colvarmodule::fatal_error().

virtual std::string colvarproxy::input_prefix (   )  [pure virtual]
 

Prefix to be used for input files (restarts, not configuration).

Implemented in colvarproxy_namd.

Referenced by colvarmodule::colvarmodule().

void colvarproxy::load_atoms (  char const *  filename,
std::vector< cvm::atom > &  atoms,
std::string const   pdb_field = "O",
double const   pdb_field_value = 0.0
)  [inline, virtual]
 

Read atom identifiers from a file.

Parameters:
filename name of the file (usually a PDB)
atoms array to which atoms read from "filename" will be appended
pdb_field (optiona) if "filename" is a PDB file, use this field to determine which are the atoms to be set

Reimplemented in colvarproxy_namd.

Definition at line 131 of file colvarproxy.h.

References colvarmodule::fatal_error().

Referenced by colvarmodule::load_atoms().

00135 {
00136   cvm::fatal_error ("Error: colvarproxy::load_atoms() has not been (re)redefined, "
00137                     "__FILE__ at line __LINE__.\n");
00138 }

void colvarproxy::load_coords (  char const *  filename,
std::vector< cvm::atom_pos > &  pos,
std::string const   pdb_field = "O",
double const   pdb_field_value = 0.0
)  [inline, virtual]
 

Load the coordinates for a group of atoms from a file (usually a PDB); if "pos" is already allocated, the number of its elements must match the number of atoms in "filename".

Reimplemented in colvarproxy_namd.

Definition at line 121 of file colvarproxy.h.

References colvarmodule::fatal_error().

Referenced by colvarmodule::load_coords().

00125 {
00126   cvm::fatal_error ("Error: colvarproxy::load_coords() has not been (re)redefined, "
00127                     "__FILE__ at line __LINE__.\n");
00128 }

virtual void colvarproxy::log (  std::string const &  message  )  [pure virtual]
 

Print a message to the main log.

Implemented in colvarproxy_namd.

Referenced by colvarmodule::log().

virtual std::string colvarproxy::output_prefix (   )  [pure virtual]
 

Prefix to be used for output files (final system configuration).

Implemented in colvarproxy_namd.

Referenced by colvarmodule::colvarmodule().

virtual cvm::real colvarproxy::position_dist2 (  cvm::atom_pos const &  pos1,
cvm::atom_pos const &  pos2
)  [pure virtual]
 

Get the square distance between two positions (with periodic boundary conditions handled transparently).

Note: in the case of periodic boundary conditions, this provides an analytical square distance (while taking the square of position_distance() would produce leads to a cusp)

Implemented in colvarproxy_namd.

Referenced by colvarmodule::position_dist2().

virtual cvm::rvector colvarproxy::position_distance (  cvm::atom_pos const &  pos1,
cvm::atom_pos const &  pos2
)  [pure virtual]
 

Get the simple distance vector between two positions (with periodic boundary conditions handled transparently).

Implemented in colvarproxy_namd.

Referenced by colvarmodule::position_distance().

virtual size_t colvarproxy::restart_frequency (   )  [pure virtual]
 

Restarts will be fritten each time this number of steps has passed.

Implemented in colvarproxy_namd.

Referenced by colvarmodule::colvarmodule().

virtual std::string colvarproxy::restart_output_prefix (   )  [pure virtual]
 

Prefix to be used for output restart files.

Implemented in colvarproxy_namd.

Referenced by colvarmodule::colvarmodule().

virtual void colvarproxy::select_closest_image (  cvm::atom_pos &  pos,
cvm::atom_pos const &  ref_pos
)  [pure virtual]
 

Get the closest periodic image to a reference position.

Parameters:
pos The position to look for the closest periodic image
ref_pos The reference position

Implemented in colvarproxy_namd.

Referenced by colvarmodule::select_closest_image(), and select_closest_images().

void colvarproxy::select_closest_images (  std::vector< cvm::atom_pos > &  pos,
cvm::atom_pos const &  ref_pos
)  [inline]
 

Perform select_closest_image() on a set of atomic positions.

After that, distance vectors can then be calculated directly, without using position_distance()

Definition at line 111 of file colvarproxy.h.

References colvarmodule::atom_pos, and select_closest_image().

Referenced by colvarmodule::select_closest_images().

00113 {
00114   for (std::vector<cvm::atom_pos>::iterator pi = pos.begin();
00115        pi != pos.end(); pi++) {
00116     select_closest_image (*pi, ref_pos);
00117   }
00118 }

virtual cvm::real colvarproxy::temperature (   )  [pure virtual]
 

Temperature of the simulation (K).

Implemented in colvarproxy_namd.

Referenced by colvarmodule::temperature().

virtual cvm::real colvarproxy::unit_angstrom (   )  [pure virtual]
 

Value of the unit for atomic coordinates with respect to angstroms (used by some variables for hard-coded default values).

Implemented in colvarproxy_namd.

Referenced by colvarmodule::unit_angstrom().

Member Data Documentation

colvarmodule* colvarproxy::colvars
 

Pointer to the instance of colvarmodule.

Definition at line 17 of file colvarproxy.h.

The documentation for this class was generated from the following file:
Generated on Mon Nov 23 04:59:34 2009 for NAMD by  doxygen 1.3.9.1