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fix_colvars.h
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Mon, Jul 22, 22:36

fix_colvars.h
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(colvars,FixColvars)
#else
#ifndef LMP_FIX_COLVARS_H
#define LMP_FIX_COLVARS_H
#include "fix.h"
#include <vector>
// forward declaration
class colvarproxy_lammps;
struct commdata;
namespace LAMMPS_NS {
class FixColvars : public Fix {
public:
FixColvars(class LAMMPS *, int, char **);
virtual ~FixColvars();
virtual int setmask();
virtual void init();
virtual void setup(int);
virtual void min_setup(int vflag) {setup(vflag);};
virtual void min_post_force(int);
virtual void post_force(int);
virtual void post_force_respa(int, int, int);
virtual void end_of_step();
virtual double compute_scalar();
virtual double memory_usage();
virtual void write_restart(FILE *);
virtual void restart(char *);
protected:
class colvarproxy_lammps *proxy; // pointer to the colvars proxy class
char *conf_file; // name of colvars config file
char *inp_name; // name/prefix of colvars restart file
char *out_name; // prefix string for all output files
char *tmp_name; // name of thermostat fix.
int rng_seed; // seed to initialize random number generator
int tstat_id; // id of the thermostat fix
double energy; // biasing energy of the fix
int me; // my MPI rank in this "world".
int num_coords; // total number of atoms controlled by this fix
tagint *taglist; // list of all atom IDs referenced by colvars.
// TODO get rid of these
// std::vector<cvm::atom_pos> *coords; // coordinates of colvar atoms
// std::vector<cvm::rvector> *forces; // received forces of colvar atoms
// std::vector<cvm::rvector> *oforce; // old total forces of colvar atoms
// std::vector<cvm::real> *masses;
// std::vector<cvm::real> *charges;
int nmax; // size of atom communication buffer.
int size_one; // bytes per atom in communication buffer.
struct commdata *comm_buf; // communication buffer
double *force_buf; // communication buffer
void *idmap; // hash for mapping atom indices to consistent order.
int *rev_idmap; // list of the hash keys for reverse mapping.
int nlevels_respa; // flag to determine respa levels.
int store_forces; // flag to determine whether to store total forces
int unwrap_flag; // 1 if atom coords are unwrapped, 0 if not
int init_flag; // 1 if initialized, 0 if not
static int instances; // count fix instances, since colvars currently
// only supports one instance at a time
MPI_Comm root2root; // inter-root communicator for multi-replica support
void one_time_init(); // one time initialization
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Cannot use fix colvars for atoms with rmass attribute
The colvars library assigns atom masses per atom type, thus atom styles
which allow setting individual per atom masses are not supported.
E: Missing argument to keyword
Self-explanatory. A keyword was recognized, but no corresponding value
found. Check the input script syntax and compare to the documentation
for the command.
E: Incorrect fix colvars unwrap flag
Self-explanatory. Check the input script syntax.
E: Unknown fix colvars parameter
Self-explanatory. Check your input script syntax.
E: Cannot use fix colvars without atom IDs
Atom IDs are not defined, but fix colvars needs them to identify an atom.
E: Fix colvars requires an atom map
Use the atom_modify command to create an atom map.
W: Using fix colvars with minimization
Some of the functionality supported with the colvars library is not
meaningful with minimization calculations.
E: Could not find tstat fix ID
Self-explanatory. The thermostat fix ID provided with the tstat keyword
is not defined (yet or anymore). Check your input file.
E: Run aborted on request from colvars module
Some error condition happened inside the colvars library that prohibits
it from continuing. Please examine the output for additional information.
*/

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