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fix_correlator.h
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fix_correlator.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 FIX_CLASS
FixStyle(correlator,FixCorrelator)
#else
#ifndef LMP_FIX_CORRELATOR_H
#define LMP_FIX_CORRELATOR_H
#include "stdio.h"
#include "fix.h"
namespace LAMMPS_NS {
/* -*- c++ -*- ---------------------------------------------------
Scalar Correlator f(tau)=<A(t)A(t+tau)> and
Cross-correlator f(tau)=<A(t)B(t+tau)>
Structure and syntax of fix inspired by fix_ave_correlate
J. Chem. Phys. 133, 154103 (2010)
Contributing authors:
Jorge Ramirez (jorge.ramirez@upm.es, Universidad Politecnica de Madrid),
Alexei Likhtman (University of Reading)
------------------------------------------------------------------ */
class FixCorrelator : public Fix {
public:
FixCorrelator(class LAMMPS *, int, char **);
~FixCorrelator();
int setmask();
void init();
void setup(int);
void end_of_step();
void write_restart(FILE *);
void restart(char *);
double memory_usage();
double *t; // Time steps for result arrays
double **f; // Result arrays
unsigned int npcorr;
private:
// NOT OPTIMAL: shift2 and accumulator2 only needed in cross-correlations
double ***shift, *** shift2;
double ***correlation;
double **accumulator, **accumulator2;
unsigned long int **ncorrelation;
unsigned int *naccumulator;
unsigned int *insertindex;
unsigned int numcorrelators; // Recommended 20
unsigned int p; // Points per correlator (recommended 16)
unsigned int m; // Num points for average (recommended 2; p mod m = 0)
unsigned int dmin; // Min distance between ponts for correlators k>0; dmin=p/m
unsigned int length; // Length of result arrays
unsigned int kmax; // Maximum correlator attained during simulation
int me,nvalues;
int nfreq;
bigint nvalid,nvalid_last;
int *which,*argindex,*value2index;
char **ids;
FILE *fp;
int type,startstep,overwrite;
long filepos;
int npair; // number of correlation pairs to calculate
double *values;
void accumulate();
void evaluate();
bigint nextvalid();
void add(const int i, const double w, const unsigned int k = 0);
void add(const int i, const double wA, const double wB, const unsigned int k = 0);
};
}
#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 open fix correlator file %s
The specified file cannot be opened. Check that the path and name are
correct.
E: Compute ID for fix correlator does not exist
Self-explanatory.
E: Fix correlator compute does not calculate a scalar
Self-explanatory.
E: Fix correlator compute does not calculate a vector
Self-explanatory.
E: Fix correlator compute vector is accessed out-of-range
The index for the vector is out of bounds.
E: Fix ID for fix correlator does not exist
Self-explanatory.
E: Fix correlator fix does not calculate a scalar
Self-explanatory.
E: Fix correlator fix does not calculate a vector
Self-explanatory.
E: Fix correlator fix vector is accessed out-of-range
The index for the vector is out of bounds.
E: Fix for fix correlator not computed at compatible time
Fixes generate their values on specific timesteps. Fix correlator
is requesting a value on a non-allowed timestep.
E: Variable name for fix correlator does not exist
Self-explanatory.
E: Fix correlator variable is not equal-style variable
Self-explanatory.
E: Invalid timestep reset for fix correlator
Resetting the timestep has invalidated the sequence of timesteps this
fix needs to process.
*/

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