This file is indexed.

/usr/include/liggghts/dump_custom.h is in libliggghts-dev 2.3.8-1build1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
/* ----------------------------------------------------------------------
   LIGGGHTS - LAMMPS Improved for General Granular and Granular Heat
   Transfer Simulations

   LIGGGHTS is part of the CFDEMproject
   www.liggghts.com | www.cfdem.com

   This file was modified with respect to the release in LAMMPS
   Modifications are Copyright 2009-2012 JKU Linz
                     Copyright 2012-     DCS Computing GmbH, Linz

   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 directory.
------------------------------------------------------------------------- */

#ifdef DUMP_CLASS

DumpStyle(custom,DumpCustom)

#else

#ifndef LMP_DUMP_CUSTOM_H
#define LMP_DUMP_CUSTOM_H

#include "dump.h"

namespace LAMMPS_NS {

class DumpCustom : public Dump {
 public:
  DumpCustom(class LAMMPS *, int, char **);
  virtual ~DumpCustom();

 protected:
  int nevery;                // dump frequency to check Fix against
  char *label;               // string for dump file header 
  int iregion;               // -1 if no region, else which region
  char *idregion;            // region ID
  int nthresh;               // # of defined threshholds
  int *thresh_array;         // array to threshhhold on for each nthresh
  int *thresh_op;            // threshhold operation for each nthresh
  double *thresh_value;      // threshhold value for each nthresh

  int *vtype;                // type of each vector (INT, DOUBLE)
  char **vformat;            // format string for each vector element

  char *columns;             // column labels

  int nchoose;               // # of selected atoms
  int maxlocal;              // size of atom selection and variable arrays
  int *choose;               // local indices of selected atoms
  double *dchoose;           // value for each atom to threshhold against
  int *clist;                // compressed list of indices of selected atoms

  int nfield;                // # of keywords listed by user
  int ioptional;             // index of start of optional args

  int *field2index;          // which compute,fix,variable calcs this field
  int *argindex;             // index into compute,fix scalar_atom,vector_atom
                             // 0 for scalar_atom, 1-N for vector_atom values

  int ncompute;              // # of Compute objects used by dump
  char **id_compute;         // their IDs
  class Compute **compute;   // list of ptrs to the Compute objects

  int nfix;                  // # of Fix objects used by dump
  char **id_fix;             // their IDs
  class Fix **fix;           // list of ptrs to the Fix objects

  int nvariable;             // # of Variables used by dump
  char **id_variable;        // their names
  int *variable;             // list of indices for the Variables
  double **vbuf;             // local storage for variable evaluation

  int ntypes;                // # of atom types
  char **typenames;             // array of element names for each type

  // private methods

  virtual void init_style();
  virtual void write_header(bigint);
  int count();
  void pack(int *);
  virtual void write_data(int, double *);
  bigint memory_usage();

  int parse_fields(int, char **);
  int add_compute(char *);
  int add_fix(char *);
  int add_variable(char *);
  virtual int modify_param(int, char **);

  typedef void (DumpCustom::*FnPtrHeader)(bigint);
  FnPtrHeader header_choice;           // ptr to write header functions
  void header_binary(bigint);
  void header_binary_triclinic(bigint);
  void header_item(bigint);
  void header_item_triclinic(bigint);

  typedef void (DumpCustom::*FnPtrData)(int, double *);
  FnPtrData write_choice;              // ptr to write data functions
  void write_binary(int, double *);
  void write_text(int, double *);

  // customize by adding a method prototype

  typedef void (DumpCustom::*FnPtrPack)(int);
  FnPtrPack *pack_choice;              // ptrs to pack functions

  void pack_compute(int);
  void pack_fix(int);
  void pack_variable(int);

  void pack_id(int);
  void pack_molecule(int);
  void pack_type(int);
  void pack_mass(int);

  void pack_x(int);
  void pack_y(int);
  void pack_z(int);
  void pack_xs(int);
  void pack_ys(int);
  void pack_zs(int);
  void pack_xs_triclinic(int);
  void pack_ys_triclinic(int);
  void pack_zs_triclinic(int);
  void pack_xu(int);
  void pack_yu(int);
  void pack_zu(int);
  void pack_xu_triclinic(int);
  void pack_yu_triclinic(int);
  void pack_zu_triclinic(int);
  void pack_xsu(int);
  void pack_ysu(int);
  void pack_zsu(int);
  void pack_xsu_triclinic(int);
  void pack_ysu_triclinic(int);
  void pack_zsu_triclinic(int);
  void pack_ix(int);
  void pack_iy(int);
  void pack_iz(int);

  void pack_vx(int);
  void pack_vy(int);
  void pack_vz(int);
  void pack_fx(int);
  void pack_fy(int);
  void pack_fz(int);
  void pack_q(int);
  void pack_density(int); 
  void pack_p(int);       
  void pack_rho(int);     
  void pack_mux(int);
  void pack_muy(int);
  void pack_muz(int);
  void pack_mu(int);
  void pack_radius(int);
  void pack_diameter(int);

  void pack_omegax(int);
  void pack_omegay(int);
  void pack_omegaz(int);
  void pack_angmomx(int);
  void pack_angmomy(int);
  void pack_angmomz(int);
  void pack_tqx(int);
  void pack_tqy(int);
  void pack_tqz(int);
  void pack_spin(int);
  void pack_eradius(int);
  void pack_ervel(int);
  void pack_erforce(int);
};

}

#endif
#endif

/* ERROR/WARNING messages:

E: No dump custom arguments specified

The dump custom command requires that atom quantities be specified to
output to dump file.

E: Invalid attribute in dump custom command

Self-explantory.

E: Could not find dump custom compute ID

The compute ID needed by dump custom to compute a per-atom quantity
does not exist.

E: Could not find dump custom fix ID

Self-explanatory.

E: Dump custom and fix not computed at compatible times

The fix must produce per-atom quantities on timesteps that dump custom
needs them.

E: Could not find dump custom variable name

Self-explanatory.

E: Region ID for dump custom does not exist

Self-explanatory.

E: Threshhold for an atom property that isn't allocated

A dump threshhold has been requested on a quantity that is
not defined by the atom style used in this simulation.

E: Dumping an atom property that isn't allocated

The chosen atom style does not define the per-atom quantity being
dumped.

E: Dumping an atom quantity that isn't allocated

Only per-atom quantities that are defined for the atom style being
used are allowed.

E: Dump custom compute does not compute per-atom info

Self-explanatory.

E: Dump custom compute does not calculate per-atom vector

Self-explanatory.

E: Dump custom compute does not calculate per-atom array

Self-explanatory.

E: Dump custom compute vector is accessed out-of-range

Self-explanatory.

E: Dump custom fix does not compute per-atom info

Self-explanatory.

E: Dump custom fix does not compute per-atom vector

Self-explanatory.

E: Dump custom fix does not compute per-atom array

Self-explanatory.

E: Dump custom fix vector is accessed out-of-range

Self-explanatory.

E: Dump custom variable is not atom-style variable

Only atom-style variables generate per-atom quantities, needed for
dump output.

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: Dump_modify region ID does not exist

Self-explanatory.

E: Dump modify element names do not match atom types

Number of element names must equal number of atom types.

E: Invalid attribute in dump modify command

Self-explantory.

E: Could not find dump modify compute ID

Self-explanatory.

E: Dump modify compute ID does not compute per-atom info

Self-explanatory.

E: Dump modify compute ID does not compute per-atom vector

Self-explanatory.

E: Dump modify compute ID does not compute per-atom array

Self-explanatory.

E: Dump modify compute ID vector is not large enough

Self-explanatory.

E: Could not find dump modify fix ID

Self-explanatory.

E: Dump modify fix ID does not compute per-atom info

Self-explanatory.

E: Dump modify fix ID does not compute per-atom vector

Self-explanatory.

E: Dump modify fix ID does not compute per-atom array

Self-explanatory.

E: Dump modify fix ID vector is not large enough

Self-explanatory.

E: Could not find dump modify variable name

Self-explanatory.

E: Dump modify variable is not atom-style variable

Self-explanatory.

E: Invalid dump_modify threshhold operator

Operator keyword used for threshold specification in not recognized.

*/