forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3320 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
parent
4615e25278
commit
fa3a647a74
|
@ -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)
|
||||
|
||||
|
|
|
@ -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.
|
||||
|
|
|
@ -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)
|
||||
|
|
|
@ -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
|
|
@ -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.
|
File diff suppressed because it is too large
Load Diff
|
@ -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:
|
||||
|
|
@ -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
|
|
@ -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"
|
||||
|
|
Loading…
Reference in New Issue