git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12720 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/USER-MISC/README

@@ -35,6 +35,7 @@ dihedral_style nharmonic, Loukas Peristeras, loukas.peristeras at scienomics.com
 dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
 dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
+fix ave/spatial/sphere, Niall Jackson (Imperial College), niall.jackson at gmail.com, 18 Nov 14
 fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
 fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
 fix ti/rs, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013

src/USER-MISC/fix_ave_spatial_sphere.h

@@ -0,0 +1,192 @@
+/* ----------------------------------------------------------------------
+   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.
+
+*/