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neb.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.
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(neb,NEB)
#else
#ifndef LMP_NEB_H
#define LMP_NEB_H
#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
class NEB : protected Pointers {
public:
NEB(class LAMMPS *);
NEB(class LAMMPS *, double, double, int, int, int, double *, double *);
~NEB();
void command(int, char **); // process neb command
void run(); // run NEB
double ebf,ebr; // forward and reverse energy barriers
private:
int me,me_universe; // my proc ID in world and universe
int ireplica,nreplica;
MPI_Comm uworld;
MPI_Comm roots; // MPI comm with 1 root proc from each world
FILE *fp;
int compressed;
double etol; // energy tolerance convergence criterion
double ftol; // force tolerance convergence criterion
int n1steps, n2steps; // number of steps in stage 1 and 2
int nevery; // output interval
char *infile; // name of file containing final state
class FixNEB *fneb;
int nall; // per-replica dimension of array all
double **all; // PE,plen,nlen,gradvnorm from each replica
double *rdist; // normalize reaction distance, 0 to 1
void readfile(char *, int);
void open(char *);
void print_status();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: NEB command before simulation box is defined
Self-explanatory.
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 NEB with a single replica
Self-explanatory.
E: Can only use NEB with 1-processor replicas
This is current restriction for NEB as implemented in LAMMPS.
E: Cannot use NEB with atom_modify sort enabled
This is current restriction for NEB implemented in LAMMPS.
E: Cannot use NEB unless atom map exists
Use the atom_modify command to create an atom map.
E: NEB requires use of fix neb
Self-explanatory.
E: NEB requires damped dynamics minimizer
Use a different minimization style.
E: Too many timesteps for NEB
You must use a number of timesteps that fit in a 32-bit integer
for NEB.
E: Too many timesteps
The cumulative timesteps must fit in a 64-bit integer.
E: Unexpected end of neb file
A read operation from the file failed.
E: Incorrect atom format in neb file
The number of fields per line is not what expected.
E: Invalid atom IDs in neb file
An ID in the file was not found in the system.
E: Cannot open gzipped file
LAMMPS was compiled without support for reading and writing gzipped
files through a pipeline to the gzip program with -DLAMMPS_GZIP.
E: Cannot open file %s
The specified file cannot be opened. Check that the path and name are
correct. If the file is a compressed file, also check that the gzip
executable can be found and run.
*/

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