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lammps/src/USER-MISC/fix_ave_spatial_sphere.h
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fix_ave_spatial_sphere.h
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* Adapted from fix ave/spatial by Niall Jackson <niall.jackson@gmail.com>*/
#ifdef FIX_CLASS
FixStyle(ave/spatial/sphere,FixAveSpatialSphere)
#else
#ifndef LMP_FIX_AVE_SPATIAL_SPHERE_H
#define LMP_FIX_AVE_SPATIAL_SPHERE_H
#include "stdio.h"
#include "fix.h"
namespace LAMMPS_NS {
class FixAveSpatialSphere : public Fix {
public:
FixAveSpatialSphere(class LAMMPS *, int, char **);
~FixAveSpatialSphere();
int setmask();
void init();
void setup(int);
void end_of_step();
double memory_usage();
double compute_array(int,int);
void reset_timestep(bigint);
private:
int me; //rank of the MPI Process
int nfreq; //fix nfreq parameter
int nrepeat; //fix nrepeat parameter
bigint nvalid; //the next timestep on which I'll be invoked
//controls for various optional behaviours
int normflag; //what type of normalisation to do
int norm;
int scaleflag; //default units (lattice, box, etc.)
double scale; //coordinate scaling factor
int regionflag; //restricted to a particular region?
char *idregion; //name of the region to use
class Region *region; //pointer to the region
FILE *fp; //pointer for the output file
long int filepos; //file position pointer
int ave; //averaging mode
int nwindow; //number of averaging windows
int iwindow; //current window
int window_limit;
int overwrite; //continuously overwrite the output (requires ave running)
//used to keep track of which per-atom values we deal with
int nvalues; //number of variables to average
int *argindex; //if the variable is an array, this is the offset in that array
int *value2index;
int *which; //what sort of variable is arg i? Variable, compute, etc?
char **ids; //names of the variables
int maxvar; //current size of the varatom array
double* varatom; //contains the peratom values of a variable
//details of the sphere and the bins
int maxbin; //current number of bins in memory (relevant if box changes)
int nbins; //number of spherical bins
int maxatom; //current size of the bin array
int *bin; //stores the bin of each atom
double *coord; //values of r at the mid points of the bins
double *binvol; //volumes of the bins
double *count_one, *count_many, *count_sum, *count_total; //bin populations
double **values_one, **values_many, **values_sum, **values_total; //accumulated bin values
double origin[3]; //origin coordinates of the sphere
int origin_type[3]; //are origin coordinates constant or variable?
char *origin_ids[3]; //store the names of variables used to access the origin
int origin_index[3]; //indices for the origin variables
int origin_val2idx[3]; //compute/variable indices
double r_min, r_minsq; //minimum radius, and its square
double r_max, r_maxsq; //maximum radius, and its square
double deltar, inv_deltar; //radial width of a bin, and its inverse (and their squares)
void setup_bins(); //create the bin arrays
void set_bin_volumes(); //calculate the volume of each bin
void bin_atoms(); //put the atom into bins based on their coordinates
bigint nextvalid(); //return the next timestep on which this is invoked
//NEED TO BE CATEGORISED
int irepeat;
double **count_list;
double ***values_list;
};
}
#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: Region ID for fix ave/spatial/spherical does not exist
Self-explanatory.
E: Cannot open fix ave/spatial/spherical file %s
The specified file cannot be opened. Check that the path and name are
correct.
E: Compute ID for fix ave/spatial/spherical does not exist
Self-explanatory.
E: Fix ave/spatial/spherical compute does not calculate per-atom values
A compute used by fix ave/spatial/spherical must generate per-atom values.
E: Fix ave/spatial/spherical compute does not calculate a per-atom vector
A compute used by fix ave/spatial/spherical must generate per-atom values.
E: Fix ave/spatial/spherical compute does not calculate a per-atom array
Self-explanatory.
E: Fix ave/spatial/spherical compute vector is accessed out-of-range
The index for the vector is out of bounds.
E: Fix ID for fix ave/spatial/spherical does not exist
Self-explanatory.
E: Fix ave/spatial/spherical fix does not calculate per-atom values
A fix used by fix ave/spatial/spherical must generate per-atom values.
E: Fix ave/spatial/spherical fix does not calculate a per-atom vector
A fix used by fix ave/spatial/spherical must generate per-atom values.
E: Fix ave/spatial/spherical fix does not calculate a per-atom array
Self-explanatory.
E: Fix ave/spatial/spherical fix vector is accessed out-of-range
The index for the vector is out of bounds.
E: Variable name for fix ave/spatial/spherical does not exist
Self-explanatory.
E: Fix ave/spatial/spherical variable is not atom-style variable
A variable used by fix ave/spatial/spherical must generate per-atom values.
E: Fix ave/spatial/spherical for triclinic boxes requires units reduced
Self-explanatory.
E: Fix ave/spatial/spherical requires reduced units if the box changes size.
If the box size changes, only the units reduced option can be
used.
E: Fix for fix ave/spatial/spherical not computed at compatible time
Fixes generate their values on specific timesteps. Fix ave/spatial/spherical is
requesting a value on a non-allowed timestep.
E: Fix ave/spatial/spherical missed timestep
You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
*/
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