git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10935 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_start.html

@@ -189,6 +189,7 @@ within the LAMMPS code.  The options that are currently recogized are:
 <UL><LI>-DLAMMPS_GZIP
 <LI>-DLAMMPS_JPEG
 <LI>-DLAMMPS_PNG
+<LI>-DLAMMPS_FFMPEG
 <LI>-DLAMMPS_MEMALIGN
 <LI>-DLAMMPS_XDR
 <LI>-DLAMMPS_SMALLBIG
@@ -200,18 +201,25 @@ within the LAMMPS code.  The options that are currently recogized are:
 <LI>-DPACK_MEMCPY 
 </UL>
 <P>The read_data and dump commands will read/write gzipped files if you
-compile with -DLAMMPS_GZIP.  It requires that your Unix support the
+compile with -DLAMMPS_GZIP.  It requires that your machine supports
-"popen" command.
+the "popen" function in the standard runtime library and that a gzip
+executable can be found by LAMMPS during a run.
 </P>
-<P>If you use -DLAMMPS_JPEG, the <A HREF = "dump.html">dump image</A> command will be
+<P>If you use -DLAMMPS_JPEG, the <A HREF = "dump_image.html">dump image</A> command
-able to write out JPEG image files. For JPEG files, you must also link
+will be able to write out JPEG image files. For JPEG files, you must
-LAMMPS with a JPEG library, as described below. If you use
+also link LAMMPS with a JPEG library, as described below. If you use
 -DLAMMPS_PNG, the <A HREF = "dump.html">dump image</A> command will be able to write
 out PNG image files.  For PNG files, you must also link LAMMPS with a
 PNG library, as described below.  If neither of those two defines are
-used, LAMMPS will only be able to write out text-based PPM image
+used, LAMMPS will only be able to write out uncompressed PPM image
 files.
 </P>
+<P>If you use -DLAMMPS_FFMPEG, the <A HREF = "dump_image.html">dump movie</A> command
+will be available to support on-the-fly generation of rendered movies
+the need to store intermediate image files. It requires that your
+machines supports the "popen" function in the standard runtime library
+and that an FFmpeg executable can be found by LAMMPS during the run.
+</P>
 <P>Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
 posix_memalign() call instead of malloc() when large chunks or memory
 are allocated by LAMMPS.  This can help to make more efficient use of

doc/Section_start.txt

@@ -183,6 +183,7 @@ within the LAMMPS code.  The options that are currently recogized are:
 -DLAMMPS_GZIP
 -DLAMMPS_JPEG
 -DLAMMPS_PNG
+-DLAMMPS_FFMPEG
 -DLAMMPS_MEMALIGN
 -DLAMMPS_XDR
 -DLAMMPS_SMALLBIG
@@ -194,18 +195,25 @@ within the LAMMPS code.  The options that are currently recogized are:
 -DPACK_MEMCPY :ul
 
 The read_data and dump commands will read/write gzipped files if you
-compile with -DLAMMPS_GZIP.  It requires that your Unix support the
+compile with -DLAMMPS_GZIP.  It requires that your machine supports
-"popen" command.
+the "popen" function in the standard runtime library and that a gzip
+executable can be found by LAMMPS during a run.
 
-If you use -DLAMMPS_JPEG, the "dump image"_dump.html command will be
+If you use -DLAMMPS_JPEG, the "dump image"_dump_image.html command
-able to write out JPEG image files. For JPEG files, you must also link
+will be able to write out JPEG image files. For JPEG files, you must
-LAMMPS with a JPEG library, as described below. If you use
+also link LAMMPS with a JPEG library, as described below. If you use
 -DLAMMPS_PNG, the "dump image"_dump.html command will be able to write
 out PNG image files.  For PNG files, you must also link LAMMPS with a
 PNG library, as described below.  If neither of those two defines are
-used, LAMMPS will only be able to write out text-based PPM image
+used, LAMMPS will only be able to write out uncompressed PPM image
 files.
 
+If you use -DLAMMPS_FFMPEG, the "dump movie"_dump_image.html command
+will be available to support on-the-fly generation of rendered movies
+the need to store intermediate image files. It requires that your
+machines supports the "popen" function in the standard runtime library
+and that an FFmpeg executable can be found by LAMMPS during the run.
+
 Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
 posix_memalign() call instead of malloc() when large chunks or memory
 are allocated by LAMMPS.  This can help to make more efficient use of

doc/dump.html

@@ -97,8 +97,8 @@
 dump 2 subgroup atom 50 dump.run.bin
 dump 4a all custom 100 dump.myforce.* id type x y vx fx
 dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
-dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
+dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
-dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress<B>2</B>
+dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress<B>2</B>
 dump 1 all xtc 1000 file.xtc
 dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce 
 </PRE>
@@ -237,9 +237,9 @@ extended CFG format files, as used by the
 package.  Since the extended CFG format uses a single snapshot of the
 system per file, a wildcard "*" must be included in the filename, as
 discussed below.  The list of atom attributes for style <I>cfg</I> must
-begin with either "id type xs ys zs" or "id type xsu ysu zsu" or 
+begin with either "mass type xs ys zs" or "mass type xsu ysu zsu" 
 since these quantities are needed to
-write the CFG files in the appropriate format (though the "id" and
+write the CFG files in the appropriate format (though the "mass" and
 "type" fields do not appear explicitly in the file).  Any remaining
 attributes will be stored as "auxiliary properties" in the CFG files.
 Note that you will typically want to use the <A HREF = "dump_modify.html">dump_modify

doc/dump.txt

@@ -85,8 +85,8 @@ dump myDump all atom 100 dump.atom
 dump 2 subgroup atom 50 dump.run.bin
 dump 4a all custom 100 dump.myforce.* id type x y vx fx
 dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke
-dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
+dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
-dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress[2]
+dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
 dump 1 all xtc 1000 file.xtc
 dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce :pre
 
@@ -225,9 +225,9 @@ extended CFG format files, as used by the
 package.  Since the extended CFG format uses a single snapshot of the
 system per file, a wildcard "*" must be included in the filename, as
 discussed below.  The list of atom attributes for style {cfg} must
-begin with either "id type xs ys zs" or "id type xsu ysu zsu" or 
+begin with either "mass type xs ys zs" or "mass type xsu ysu zsu" 
 since these quantities are needed to
-write the CFG files in the appropriate format (though the "id" and
+write the CFG files in the appropriate format (though the "mass" and
 "type" fields do not appear explicitly in the file).  Any remaining
 attributes will be stored as "auxiliary properties" in the CFG files.
 Note that you will typically want to use the "dump_modify

doc/fix_phonon.html

@@ -25,8 +25,14 @@
 
 <LI>Nwait = wait this many timesteps before measuring 
 
-<LI>map_file = file containing the mapping info between atom ID and the lattice indices 
+<LI>map_file = <I>file</I> or <I>GAMMA</I> 
 
+<PRE>  <I>file</I> is the file that contains the mapping info between atom ID and the lattice indices. 
+</PRE>
+<PRE>  <I>GAMMA</I> flags to treate the whole simulation box as a unit cell, so that the mapping
+  info can be generated internally. In this case, dynamical matrix at only the gamma-point
+  will/can be evaluated. 
+</PRE>
 <LI>prefix = prefix for output files 
 
 <LI>one or none keyword/value pairs may be appended 
@@ -43,7 +49,8 @@
 <P><B>Examples:</B>
 </P>
 <PRE>fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1
-fix 1 all phonon 20 5000 200000 map.in EAM3D 
+fix 1 all phonon 20 5000 200000 map.in EAM3D
+fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -124,6 +131,13 @@ which lattice point; the lattice indices start from 0. An auxiliary
 code, <A HREF = "http://code.google.com/p/latgen">latgen</A>, can be employed to
 generate the compatible map file for various crystals.
 </P>
+<P>In case one simulates an aperiodic system, where the whole simulation box
+is treated as a unit cell, one can set <I>map_file</I> as <I>GAMMA</I>, so that the mapping
+info will be generated internally and a file is not needed. In this case, the
+dynamical matrix at only the gamma-point will/can be evaluated. Please keep in
+mind that fix-phonon is designed for cyrstals, it will be inefficient and
+even degrade the performance of lammps in case the unit cell is too large.
+</P>
 <P>The calculated dynamical matrix elements are written out in
 <A HREF = "units.html">energy/distance^2/mass</A> units.  The coordinates for <I>q</I>
 points in the log file is in the units of the basis vectors of the

doc/fix_phonon.txt

@@ -17,7 +17,12 @@ phonon = style name of this fix command :l
 N = measure the Green's function every this many timesteps :l
 Noutput = output the dynamical matrix every this many measurements :l
 Nwait = wait this many timesteps before measuring :l
-map_file = file containing the mapping info between atom ID and the lattice indices :l
+map_file = {file} or {GAMMA} :l
+  {file} is the file that contains the mapping info between atom ID and the lattice indices. :pre
+
+  {GAMMA} flags to treate the whole simulation box as a unit cell, so that the mapping
+  info can be generated internally. In this case, dynamical matrix at only the gamma-point
+  will/can be evaluated. :pre
 prefix = prefix for output files :l
 one or none keyword/value pairs may be appended :l
 keyword = {sysdim} or {nasr} :l
@@ -30,7 +35,8 @@ keyword = {sysdim} or {nasr} :l
 [Examples:]
 
 fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1
-fix 1 all phonon 20 5000 200000 map.in EAM3D :pre
+fix 1 all phonon 20 5000 200000 map.in EAM3D
+fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 :pre
 
 [Description:]
 
@@ -111,6 +117,13 @@ which lattice point; the lattice indices start from 0. An auxiliary
 code, "latgen"_http://code.google.com/p/latgen, can be employed to
 generate the compatible map file for various crystals.
 
+In case one simulates an aperiodic system, where the whole simulation box
+is treated as a unit cell, one can set {map_file} as {GAMMA}, so that the mapping
+info will be generated internally and a file is not needed. In this case, the
+dynamical matrix at only the gamma-point will/can be evaluated. Please keep in
+mind that fix-phonon is designed for cyrstals, it will be inefficient and
+even degrade the performance of lammps in case the unit cell is too large.
+
 The calculated dynamical matrix elements are written out in
 "energy/distance^2/mass"_units.html units.  The coordinates for {q}
 points in the log file is in the units of the basis vectors of the

src/USER-PHONON/fix_phonon.h

@@ -1,185 +1,185 @@
-/* ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
-   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   www.cs.sandia.gov/~sjplimp/lammps.html
-   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
-
+
-   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-   certain rights in this software.  This software is distributed under
+   certain rights in this software.  This software is distributed under
-   the GNU General Public License.
+   the GNU General Public License.
-
+
-   See the README file in the top-level LAMMPS directory.
+   See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
+------------------------------------------------------------------------- */
-/* ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
-   Contributing authors:
+   Contributing authors:
-     Ling-Ti Kong
+     Ling-Ti Kong
-
+
-   Contact:
+   Contact:
-     School of Materials Science and Engineering,
+     School of Materials Science and Engineering,
-     Shanghai Jiao Tong University,
+     Shanghai Jiao Tong University,
-     800 Dongchuan Road, Minhang,
+     800 Dongchuan Road, Minhang,
-     Shanghai 200240, CHINA
+     Shanghai 200240, CHINA
-
+
-     konglt@sjtu.edu.cn; konglt@gmail.com
+     konglt@sjtu.edu.cn; konglt@gmail.com
-------------------------------------------------------------------------- */
+------------------------------------------------------------------------- */
-#ifdef FIX_CLASS
+#ifdef FIX_CLASS
-
+
-FixStyle(phonon,FixPhonon)
+FixStyle(phonon,FixPhonon)
-
+
-#else
+#else
-
+
-#ifndef FIX_PHONON_H
+#ifndef FIX_PHONON_H
-#define FIX_PHONON_H
+#define FIX_PHONON_H
-
+
-#include <complex>
+#include <complex>
-#include "fix.h"
+#include "fix.h"
-#include <map>
+#include <map>
-#include "stdio.h"
+#include "stdio.h"
-#include "stdlib.h"
+#include "stdlib.h"
-#include "string.h"
+#include "string.h"
-
+
-namespace LAMMPS_NS {
+namespace LAMMPS_NS {
-
+
-class FixPhonon : public Fix {
+class FixPhonon : public Fix {
- public:
+ public:
-  FixPhonon(class LAMMPS *, int, char **);
+  FixPhonon(class LAMMPS *, int, char **);
-  ~FixPhonon();
+  ~FixPhonon();
-
+
-  int  setmask();
+  int  setmask();
-  void init();
+  void init();
-  void setup(int);
+  void setup(int);
-  void end_of_step();
+  void end_of_step();
-  void post_run();
+  void post_run();
-  double memory_usage();
+  double memory_usage();
-  int modify_param(int, char **);
+  int modify_param(int, char **);
-
+
- private:
+ private:
-  int me,nprocs;
+  int me,nprocs;
-  bigint waitsteps;                             // wait these number of timesteps before recording atom positions
+  bigint waitsteps;                             // wait these number of timesteps before recording atom positions
-  bigint prev_nstep;                            // number of steps from previous run(s); to judge if waitsteps is reached.
+  bigint prev_nstep;                            // number of steps from previous run(s); to judge if waitsteps is reached.
-  int nfreq, ifreq;                             // after this number of measurement (nfreq), the result will be output once
+  int nfreq, ifreq;                             // after this number of measurement (nfreq), the result will be output once
-  int nx,ny,nz,nucell,ntotal;                   // surface dimensions in x- and y-direction, number of atom per unit surface cell
+  int nx,ny,nz,nucell,ntotal;                   // surface dimensions in x- and y-direction, number of atom per unit surface cell
-  int neval;                                    // # of evaluations
+  int neval;                                    // # of evaluations
-  int sysdim;                                   // system dimension
+  int sysdim;                                   // system dimension
-  int ngroup, nfind;                            // total number of atoms in group; total number of atoms on this proc
+  int ngroup, nfind;                            // total number of atoms in group; total number of atoms on this proc
-  char *prefix, *logfile;                       // prefix of output file names
+  char *prefix, *logfile;                       // prefix of output file names
-  FILE *flog;
+  FILE *flog;
-  
+  
-  double *M_inv_sqrt;
+  double *M_inv_sqrt;
-
+
-  class FFT3d *fft;                             // to do fft via the fft3d wraper
+  class FFT3d *fft;                             // to do fft via the fft3d wraper
-  int nxlo,nxhi,mysize;                         // size info for local MPI_FFTW
+  int nxlo,nxhi,mysize;                         // size info for local MPI_FFTW
-  int mynpt,mynq,fft_nsend;
+  int mynpt,mynq,fft_nsend;
-  int *fft_cnts, *fft_disp;
+  int *fft_cnts, *fft_disp;
-  int fft_dim, fft_dim2;
+  int fft_dim, fft_dim2;
-  double *fft_data;
+  double *fft_data;
-  
+  
-  int  itag, idx, idq;                          // index variables
+  int  itag, idx, idq;                          // index variables
-  std::map<int,int> tag2surf, surf2tag;         // Mapping info
+  std::map<int,int> tag2surf, surf2tag;         // Mapping info
-
+
-  double **RIloc;                               // R(r) and index on local proc
+  double **RIloc;                               // R(r) and index on local proc
-  double **RIall;                               // gathered R(r) and index
+  double **RIall;                               // gathered R(r) and index
-  double **Rsort;                               // sorted R(r)
+  double **Rsort;                               // sorted R(r)
-  double **Rnow;                                // Current R(r) on local proc
+  double **Rnow;                                // Current R(r) on local proc
-  double **Rsum;                                // Accumulated R(r) on local proc
+  double **Rsum;                                // Accumulated R(r) on local proc
-
+
-  int *recvcnts, *displs;                       // MPI related variables
+  int *recvcnts, *displs;                       // MPI related variables
-
+
-  std::complex<double> **Rqnow;                 // Current R(q) on local proc
+  std::complex<double> **Rqnow;                 // Current R(q) on local proc
-  std::complex<double> **Rqsum;                 // Accumulator for conj(R(q)_alpha)*R(q)_beta
+  std::complex<double> **Rqsum;                 // Accumulator for conj(R(q)_alpha)*R(q)_beta
-  std::complex<double> **Phi_q;                 // Phi's on local proc
+  std::complex<double> **Phi_q;                 // Phi's on local proc
-  std::complex<double> **Phi_all;               // Phi for all
+  std::complex<double> **Phi_all;               // Phi for all
-
+
-  void readmap();                               // to read the mapping of gf atoms
+  void readmap();                               // to read the mapping of gf atoms
-  char *mapfile;                                // file name of the map file
+  char *mapfile;                                // file name of the map file
-
+
-  void getmass();                               // to get the mass of each atom in a unit cell
+  void getmass();                               // to get the mass of each atom in a unit cell
-
+
-  int nasr;
+  int nasr;
-  void postprocess();                           // to post process the data
+  void postprocess();                           // to post process the data
-  void EnforceASR();                            // to apply acoustic sum rule to gamma point force constant matrix
+  void EnforceASR();                            // to apply acoustic sum rule to gamma point force constant matrix
-
+
-  char *id_temp;                                // compute id for temperature
+  char *id_temp;                                // compute id for temperature
-  double *TempSum;                              // to get the average temperature vector
+  double *TempSum;                              // to get the average temperature vector
-  double inv_nTemp;                             // inverse of number of atoms in temperature group
+  double inv_nTemp;                             // inverse of number of atoms in temperature group
-  class Compute *temperature;                   // compute that computes the temperature
+  class Compute *temperature;                   // compute that computes the temperature
-
+
-  double hsum[6], **basis;
+  double hsum[6], **basis;
-  int *basetype;
+  int *basetype;
-
+
-  // private methods to do matrix inversion
+  // private methods to do matrix inversion
-  void GaussJordan(int, std::complex<double>*);
+  void GaussJordan(int, std::complex<double>*);
-
+
-};
+};
-}
+}
-#endif
+#endif
-#endif
+#endif
-
+
-/* ERROR/WARNING messages:
+/* ERROR/WARNING messages:
-
+
-E: Illegal fix phonon command...
+E: Illegal fix phonon command...
-
+
-Self-explanatory.  Check the input script syntax and compare to the
+Self-explanatory.  Check the input script syntax and compare to the
-documentation for the command.  You can use -echo screen as a
+documentation for the command.  You can use -echo screen as a
-command-line option when running LAMMPS to see the offending line.
+command-line option when running LAMMPS to see the offending line.
-
+
-E: No atom found for fix phonon!
+E: No atom found for fix phonon!
-
+
-Self-explanatory. Number of atoms in the group that was passed to
+Self-explanatory. Number of atoms in the group that was passed to
-fix-phonon is less than 1.
+fix-phonon is less than 1.
-
+
-E: Can not open output file %s"
+E: Can not open output file %s"
-
+
-Self-explanatory.
+Self-explanatory.
-
+
-E: Illegal fix_modify command
+E: Illegal fix_modify command
-
+
-Self-explanatory.
+Self-explanatory.
-
+
-E: Could not find fix_modify temp ID
+E: Could not find fix_modify temp ID
-
+
-Self-explanatory.
+Self-explanatory.
-
+
-E: Fix_modify temp ID does not compute temperature
+E: Fix_modify temp ID does not compute temperature
-
+
-Self-explanatory.
+Self-explanatory.
-
+
-E: Cannot open input map file %s
+E: Cannot open input map file %s
-
+
-Self-explanatory.
+Self-explanatory.
-
+
-E: Error while reading header of mapping file!
+E: Error while reading header of mapping file!
-
+
-Self-explanatory. The first line of the map file is expected to
+Self-explanatory. The first line of the map file is expected to
-contain 4 positive integer numbers.
+contain 4 positive integer numbers.
-
+
-E: FFT mesh and number of atoms in group mismatch!
+E: FFT mesh and number of atoms in group mismatch!
-
+
-Self-explanatory. The product of the 4 numbers should be exactly the
+Self-explanatory. The product of the 4 numbers should be exactly the
-total number of atoms in the group that was passed to fix-phonon.
+total number of atoms in the group that was passed to fix-phonon.
-
+
-E: Error while reading comment of mapping file!
+E: Error while reading comment of mapping file!
-
+
-Self-explanatory. The second line of the map file should be a comment line.
+Self-explanatory. The second line of the map file should be a comment line.
-
+
-E: The mapping is incomplete!
+E: The mapping is incomplete!
-
+
-Self-explanatory.
+Self-explanatory.
-
+
-E: Error while reading mapping file!
+E: Error while reading mapping file!
-
+
-Self-explanatory.
+Self-explanatory.
-
+
-E: The mapping info read is incorrect!
+E: The mapping info read is incorrect!
-
+
-Self-explanatory.
+Self-explanatory.
-
+
-E: Singular matrix in complex GaussJordan!
+E: Singular matrix in complex GaussJordan!
-
+
-Self-explanatory.
+Self-explanatory.
-
+
-W: More than one fix phonon defined
+W: More than one fix phonon defined
-
+
-Self-explanatory. Just to warn that more than one fix-phonon is defined, but allowed.
+Self-explanatory. Just to warn that more than one fix-phonon is defined, but allowed.
-
+
-*/
+*/

src/dump_cfg.cpp

@@ -13,6 +13,7 @@
 
 /* ----------------------------------------------------------------------
    Contributing author: Liang Wan (Chinese Academy of Sciences)
+   	Memory efficiency improved by Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
 #include "math.h"
@@ -34,7 +35,7 @@
 
 using namespace LAMMPS_NS;
 
-enum{INT,DOUBLE};  // same as in dump_custom.cpp
+enum{INT,DOUBLE,STRING};   // same as in DumpCustom
 
 /* ---------------------------------------------------------------------- */
 
@@ -42,26 +43,23 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
   DumpCustom(lmp, narg, arg)
 {
   if (narg < 10 ||
-      strcmp(arg[5],"id") != 0 || strcmp(arg[6],"type") != 0 ||
+      strcmp(arg[5],"mass") != 0 || strcmp(arg[6],"type") != 0 ||
       (strcmp(arg[7],"xs") != 0 && strcmp(arg[7],"xsu") != 0) ||
       (strcmp(arg[8],"ys") != 0 && strcmp(arg[8],"ysu") != 0) ||
       (strcmp(arg[9],"zs") != 0 && strcmp(arg[9],"zsu") != 0))
     error->all(FLERR,"Dump cfg arguments must start with "
-               "'id type xs ys zs' or 'id type xsu ysu zsu'");
+               "'mass type xs ys zs' or 'mass type xsu ysu zsu'");
 
   if (strcmp(arg[7],"xs") == 0)
     if (strcmp(arg[8],"ysu") == 0 || strcmp(arg[9],"zsu") == 0)
-      error->all(FLERR,"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
+      error->all(FLERR,
+                 "Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
     else unwrapflag = 0;
   else if (strcmp(arg[8],"ys") == 0 || strcmp(arg[9],"zs") == 0)
-    error->all(FLERR,"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
+    error->all(FLERR,
+               "Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
   else unwrapflag = 1;
 
-  // arrays for data rearrangement
-
-  rbuf = NULL;
-  nchosen = nlines = 0;
-
   // setup auxiliary property name strings
   // convert 'X_ID[m]' (X=c,f,v) to 'ID_m'
 
@@ -105,8 +103,6 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
 
 DumpCFG::~DumpCFG()
 {
-  if (rbuf) memory->destroy(rbuf);
-
   if (auxname) {
     for (int i = 0; i < nfield-5; i++) delete [] auxname[i];
     delete [] auxname;
@@ -117,7 +113,8 @@ DumpCFG::~DumpCFG()
 
 void DumpCFG::init_style()
 {
-  if (multifile == 0) error->all(FLERR,"Dump cfg requires one snapshot per file");
+  if (multifile == 0) 
+    error->all(FLERR,"Dump cfg requires one snapshot per file");
 
   DumpCustom::init_style();
 }
@@ -160,78 +157,57 @@ void DumpCFG::write_header(bigint n)
   fprintf(fp,"entry_count = %d\n",nfield-2);
   for (int i = 0; i < nfield-5; i++)
     fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]);
-
-  // allocate memory needed for data rearrangement
-
-  nchosen = static_cast<int> (n);
-  if (rbuf) memory->destroy(rbuf);
-  memory->create(rbuf,nchosen,size_one,"dump:rbuf");
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   write data lines to file in a block-by-block style
-   write head of block (mass & element name) only if has atoms of the type
-------------------------------------------------------------------------- */
 
 void DumpCFG::write_data(int n, double *mybuf)
 {
-  int i,j,m,itype;
+  int i,j,m;
 
-  double *rmass = atom->rmass;
+  if (unwrapflag == 0) {
-  double *mass = atom->mass;
+    m = 0;
-
+    for (i = 0; i < n; i++) {
-  // transfer data from buf to rbuf
+      for (j = 0; j < size_one; j++) {
-  // if write by proc 0, transfer chunk by chunk
+        if (j == 0) {
-
+	  fprintf(fp,"%f \n",mybuf[m]);
-  for (i = 0, m = 0; i < n; i++) {
+        } else if (j == 1) {
-    for (j = 0; j < size_one; j++)
+	  fprintf(fp,"%s \n",typenames[(int) mybuf[m]]);
-      rbuf[nlines][j] = mybuf[m++];
+        } else if (j >= 2) {
-    nlines++;
+          if (vtype[j] == INT) 
-  }
+            fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
-
+          else if (vtype[j] == DOUBLE) 
-  // write data lines in rbuf to file after transfer is done
+            fprintf(fp,vformat[j],mybuf[m]);
-
+          else if (vtype[j] == STRING) 
-  double unwrap_coord;
+            fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
-
-  if (nlines == nchosen) {
-    for (itype = 1; itype <= ntypes; itype++) {
-      for (i = 0; i < nchosen; i++)
-        if (rbuf[i][1] == itype) break;
-      if (i < nchosen) {
-        if (rmass) fprintf(fp,"%g\n",rmass[i]);
-        else fprintf(fp,"%g\n",mass[itype]);
-        fprintf(fp,"%s\n",typenames[itype]);
-        for (; i < nchosen; i++) {
-          if (rbuf[i][1] == itype) {
-            if (unwrapflag == 0)
-              for (j = 2; j < size_one; j++) {
-                if (vtype[j] == INT)
-                  fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
-                else fprintf(fp,vformat[j],rbuf[i][j]);
-              }
-            else {
-
-              // Unwrapped scaled coordinates are shifted to
-              // center of expanded box, to prevent
-              // rewrapping by AtomEye. Dividing by
-              // expansion factor restores correct
-              // interatomic distances.
-
-              for (j = 2; j < 5; j++) {
-                unwrap_coord = (rbuf[i][j] - 0.5)/UNWRAPEXPAND + 0.5;
-                fprintf(fp,vformat[j],unwrap_coord);
-              }
-              for (j = 5; j < size_one; j++) {
-                if (vtype[j] == INT)
-                  fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
-                else fprintf(fp,vformat[j],rbuf[i][j]);
-              }
-            }
-            fprintf(fp,"\n");
-          }
         }
+        m++;
       }
+      fprintf(fp,"\n");
+    }
+  } else if (unwrapflag == 1) {
+    m = 0;
+    double unwrap_coord;
+    for (i = 0; i < n; i++) {
+      for (j = 0; j < size_one; j++) {
+        if (j == 0) {
+	  fprintf(fp,"%f \n",mybuf[m]);
+        } else if (j == 1) {
+	  fprintf(fp,"%s \n",typenames[(int) mybuf[m]]);
+        } else if (j >= 2 && j <= 4) {
+          unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
+          fprintf(fp,vformat[j],unwrap_coord);
+        } else if (j >= 5 ) {
+          if (vtype[j] == INT) 
+            fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
+          else if (vtype[j] == DOUBLE) 
+            fprintf(fp,vformat[j],mybuf[m]);
+          else if (vtype[j] == STRING) 
+            fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
+        }
+        m++;
+      }
+      fprintf(fp,"\n");
     }
-    nlines = 0;
   }
 }

src/dump_cfg.h

@@ -31,14 +31,12 @@ class DumpCFG : public DumpCustom {
 
  private:
   char **auxname;            // name strings of auxiliary properties
-  int nchosen;               // # of lines to be written on a writing proc
-  int nlines;                // # of lines transferred from buf to rbuf
-  double **rbuf;             // buf of data lines for data lines rearrangement
   int unwrapflag;            // 1 if unwrapped coordinates are requested
 
   void init_style();
   void write_header(bigint);
   void write_data(int, double *);
+
 };
 
 }

src/dump_custom.cpp

@@ -44,7 +44,7 @@ enum{ID,MOL,TYPE,ELEMENT,MASS,
      TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
      COMPUTE,FIX,VARIABLE};
 enum{LT,LE,GT,GE,EQ,NEQ};
-enum{INT,DOUBLE,STRING};
+enum{INT,DOUBLE,STRING};    // same as in DumpCFG
 
 #define INVOKED_PERATOM 8
 

tools/amber2lmp/README

@@ -8,6 +8,14 @@ dump2try99.py		same as dump2trj for LAMMPS 99 format
 
 -------------------------
 
+Modifications in file amber2lammps.py, by Vikas Varshney
+Dated Nov 4, 2013
+Email address: vv0210@gmail.com
+
+added support for flags used in current version of AMBER
+
+-------------------------
+
 Modifications in file amber2lammps.py, by Vikas Varshney
 Dated July 5, 2005
 Email address : vv5@uakron.edu

tools/amber2lmp/amber2lammps.py

@@ -8,6 +8,7 @@
 # 
 # Modified by Vikas Varshney, U Akron, 5 July 2005, as described in README
 # Bug Fixed :Third argument in Dihedral Coeffs section is an integer - Ketan S Khare September 26, 2011
+# Modified by Vikas Varshney, Oct 8, 2013 to include additional flags (Atomic_Number, Coulombic and van der Waals 1-4 factors which are included in newer vesions of .top and .crd files in amber12. 
 
 #============================================================
 
@@ -554,6 +555,11 @@ class Amber:
       	for i in range(self.NATOM):
             self.CHRG.append(eval(Pop(Item_list,0)))
 
+	print 'Reading Atomic Number...'
+        self.ANUMBER = []
+      	for i in range(self.NATOM):
+            self.ANUMBER.append(eval(Pop(Item_list,0)))
+
         print 'Reading Atomic Masses...'
 	self.AMASS = []
         for i in range(self.NATOM):
@@ -619,6 +625,16 @@ class Amber:
         for i in range(self.NPTRA):
             self.PHASE.append(eval(Pop(Item_list,0)))
         
+	print 'Reading 1-4 Electrostatic Scaling Factor...'
+        self.SCEEFAC = []
+        for i in range(self.NPTRA):
+            self.SCEEFAC.append(eval(Pop(Item_list,0)))
+        
+	print 'Reading 1-4 Van der Waals Scaling Factor...'
+        self.SCNBFAC = []
+        for i in range(self.NPTRA):
+            self.SCNBFAC.append(eval(Pop(Item_list,0)))
+        
 	print 'Reading Solty...' #I think this is currently not used in AMBER. Check it out, though
         self.SOLTY = []
         for i in range(self.NATYP):

tools/msi2lmp/README

@@ -1,6 +1,13 @@
 Stephanie Teich-McGoldrick (Sandai) is the current maintainer
 of the msi2lmp tool.  She can be contacted at steichm at sandia.gov
 
+08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Fixed a memory access violation with Class 2 force fields.
+Free all allocated memory to better detection of memory errors.
+Print out version number and data with all print levels > 0.
+Added valgrind checks to the regression tests
+
 02 Aug 2013 Axel Kohlmeyer <akohlmey@gmail.com>
 
 Added rudimentary support for OPLS-AA based on