git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3320 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/Makefile

@@ -16,7 +16,8 @@ OBJ = 	$(SRC:.cpp=.o)
 PACKAGE = asphere class2 colloid dipole dpd gpu granular \
 	  kspace manybody meam molecule opt peri poems prd reax xtc
 
-PACKUSER = user-ackland user-atc user-cd-eam user-cg-cmm user-ewaldn user-smd
+PACKUSER = user-ackland user-atc user-cd-eam user-cg-cmm user-ewaldn \
+	   user-imd user-smd
 
 PACKALL = $(PACKAGE) $(PACKUSER)
 

src/USER-ATC/README

@@ -10,3 +10,6 @@ LAMMPS input script.  This fix can be employed to either do concurrent
 coupling of MD with FE-based physics surrogates or on-the-fly
 post-processing of atomic information to continuum fields.  See the
 doc page for the fix atc command to get started.
+
+There are example scripts for using this package with LAMMPS in
+examples/USER/atc.

src/USER-CG-CMM/README

@@ -18,8 +18,8 @@ and angle_style cg/cmm.
 
 See the documentation files for these commands for details.
 
-There is also an cg-cmm example directory under examples/USER with
-sample inputs and outputs.
+There are example scripts for using this package with LAMMPS in
+examples/USER/cg-cmm.
 
 These styles allow coarse grained MD simulations with the
 parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)

src/USER-IMD/Install.csh

@@ -0,0 +1,20 @@
+# Install/unInstall package classes in LAMMPS
+
+if ($1 == 1) then
+
+  cp -p style_user_imd.h ..
+
+  cp -p fix_imd.cpp ..
+
+  cp -p fix_imd.h ..
+
+else if ($1 == 0) then
+
+  rm ../style_user_imd.h
+  touch ../style_user_imd.h
+
+  rm ../fix_imd.cpp
+
+  rm ../fix_imd.h
+
+endif

src/USER-IMD/README

@@ -0,0 +1,17 @@
+The files in this directory are a user-contributed package for LAMMPS.
+
+The person who created these files is Axel Kohlmeyer
+(axel.kohlmeyer@temple.edu).  Contact him directly if you 
+have questions or for example scripts that use it.
+
+This package implements a "fix imd" command which can be used in a
+LAMMPS input script.  IMD stands for interactive molecular dynamics,
+and allows realtime visualization and manipulation of MD simulations
+through the IMD protocol, initially implemented in VMD and NAMD.
+
+There are example scripts for using this package with LAMMPS in
+examples/USER/imd.
+
+This software includes code developed by the Theoretical and Computational 
+Biophysics Group in the Beckman Institute for Advanced Science and 
+Technology at the University of Illinois at Urbana-Champaign.

src/USER-IMD/fix_imd.h

@@ -0,0 +1,99 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   The FixIMD class contains code from VMD and NAMD which is copyrighted
+   by the Board of Trustees of the University of Illinois and is free to 
+   use with LAMMPS according to point 2 of the UIUC license (10% clause):
+
+" Licensee may, at its own expense, create and freely distribute 
+complimentary works that interoperate with the Software, directing others to 
+the TCBG server to license and obtain the Software itself. Licensee may, at 
+its own expense, modify the Software to make derivative works.  Except as 
+explicitly provided below, this License shall apply to any derivative work 
+as it does to the original Software distributed by Illinois.  Any derivative 
+work should be clearly marked and renamed to notify users that it is a 
+modified version and not the original Software distributed by Illinois.  
+Licensee agrees to reproduce the copyright notice and other proprietary 
+markings on any derivative work and to include in the documentation of such 
+work the acknowledgement:
+
+ "This software includes code developed by the Theoretical and Computational 
+  Biophysics Group in the Beckman Institute for Advanced Science and 
+  Technology at the University of Illinois at Urbana-Champaign."
+
+Licensee may redistribute without restriction works with up to 1/2 of their 
+non-comment source code derived from at most 1/10 of the non-comment source 
+code developed by Illinois and contained in the Software, provided that the 
+above directions for notice and acknowledgement are observed.  Any other 
+distribution of the Software or any derivative work requires a separate 
+license with Illinois.  Licensee may contact Illinois (vmd@ks.uiuc.edu) to 
+negotiate an appropriate license for such distribution."
+------------------------------------------------------------------------- */
+
+#ifndef FIX_IMD_H
+#define FIX_IMD_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixIMD : public Fix {
+ public:
+  FixIMD(class LAMMPS *, int, char **);
+  ~FixIMD();
+  int setmask();
+  void init();
+  void setup(int);
+  void post_force(int); 
+  void post_force_respa(int, int, int);
+  double memory_usage();
+
+ private:
+  int    imd_port;
+  void  *localsock;
+  void  *clientsock;
+  
+  int    num_coords;            // total number of atoms controlled by this fix 
+  int    size_one;              // bytes per atom in communication buffer.
+  int    maxbuf;                // size of atom communication buffer.
+  void  *comm_buf;              // communication buffer
+  void  *idmap;                 // hash for mapping atom indices to consistent order.
+  int   *rev_idmap;             // list of the hash keys for reverse mapping.
+
+  int    imd_forces;            // number of forces communicated via IMD.
+  void  *force_buf;             // force data buffer
+  double imd_fscale;            // scale factor for forces. in case VMD's units are off.
+
+  int    imd_inactive;          // true if IMD connection stopped.
+  int    imd_terminate;         // true if IMD requests termination of run.
+  int    imd_trate;             // IMD transmission rate.
+
+  int    unwrap_flag;           // true if coordinates need to be unwrapped before sending
+
+  int    me;                    // my MPI rank in this "world".
+  int    nlevels_respa;         // flag to determine respa levels.
+};
+
+}
+
+#endif
+
+// Local Variables:
+// mode: c++
+// compile-command: "make -j4 openmpi"
+// c-basic-offset: 2
+// fill-column: 76
+// indent-tabs-mode: nil
+// End:
+

src/USER-IMD/style_user_imd.h

@@ -0,0 +1,20 @@
+/* ----------------------------------------------------------------------
+   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 FixInclude
+#include "fix_imd.h"
+#endif
+
+#ifdef FixClass
+FixStyle(imd,FixIMD)
+#endif

src/style_user_packages.h

@@ -19,4 +19,5 @@
 #include "style_user_cd_eam.h"
 #include "style_user_cg_cmm.h"
 #include "style_user_ewaldn.h"
+#include "style_user_imd.h"
 #include "style_user_smd.h"