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Merge pull request #452 from akohlmey/small-fixes-and-updates 

Small fixes and updates
This commit is contained in:
sjplimp 2017-05-04 11:23:23 -06:00 committed by GitHub
parent addd87c0f7 7f49ee8fd7
commit dcc5472cba
40 changed files with 406 additions and 281 deletions
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6
doc/src/Section_errors.txt
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@ -11171,6 +11171,12 @@ Self-explanatory. :dd
If the fix changes the timestep, the dump dcd file will not
reflect the change. :dd
{Energy due to X extra global DOFs will be included in minimizer energies} :dt
When using fixes like box/relax, the potential energy used by the minimizer
is augmented by an additional energy provided by the fix. Thus the printed
converged energy may be different from the total potential energy. :dd
{Energy tally does not account for 'zero yes'} :dt
The energy removed by using the 'zero yes' flag is not accounted

9
doc/src/Section_tools.txt
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@ -369,15 +369,18 @@ supports it. It has its own WWW page at
msi2lmp tool :h4,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS input
data files from BIOVIA's Materias Studio files (formerly Accelrys'
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
Insight MD code, formerly MSI/Biosym and its Discover MD code).
This tool was written by John Carpenter (Cray), Michael Peachey
(Cray), and Steve Lustig (Dupont). Several people contributed changes
to remove bugs and adapt its output to changes in LAMMPS.
See the README file for more information.
This tool has several known limitations and is no longer under active
development, so there are no changes except for the occasional bugfix.
See the README file in the tools/msi2lmp folder for more information.
:line

1
doc/src/bonds.txt
View File

@ -16,7 +16,6 @@ Bond Styles :h1
bond_none
bond_nonlinear
bond_oxdna
bond_oxdna2
bond_quartic
bond_table
bond_zero

9
doc/src/fix_gle.txt
View File

@ -67,9 +67,10 @@ target value as the {Tstart} and {Tstop} arguments, so that the diffusion
matrix that gives canonical sampling for a given A is computed automatically.
However, the GLE framework also allow for non-equilibrium sampling, that
can be used for instance to model inexpensively zero-point energy
effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the
{noneq} keyword followed by the name of the file that contains the
static covariance matrix for the non-equilibrium dynamics.
effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq}
keyword followed by the name of the file that contains the static covariance
matrix for the non-equilibrium dynamics. Please note, that the covariance
matrix is expected to be given in [temperature units].
Since integrating GLE dynamics can be costly when used together with
simple potentials, one can use the {every} optional keyword to
@ -148,7 +149,7 @@ dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html
1170-80 (2010)
:link(GLE4MD)
[(GLE4MD)] "http://epfl-cosmo.github.io/gle4md/"_http://epfl-cosmo.github.io/gle4md/
[(GLE4MD)] "http://gle4md.org/"_http://gle4md.org/
:link(Ceriotti2)
[(Ceriotti2)] Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,

5
doc/src/improper_cossq.txt
View File

@ -45,12 +45,9 @@ above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
K (energy/radian^2)
K (energy)
X0 (degrees) :ul
X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

5
doc/src/improper_ring.txt
View File

@ -49,12 +49,9 @@ above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
K (energy/radian^2)
K (energy)
theta0 (degrees) :ul
theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

6
doc/src/pair_hybrid.txt
View File

@ -225,6 +225,12 @@ special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
pair_modify pair tersoff special lj/coul 1.0 1.0 1.0 :pre
For use with the various "compute */tally"_compute_tally.html
computes, the "pair_modify compute/tally"_pair_modify.html
command can be used to selectively turn off processing of
the compute tally styles, for example, if those pair styles
(e.g. manybody styles) do not support this feature.
See the "pair_modify"_pair_modify.html doc page for details on
the specific syntax, requirements and restrictions.

29
doc/src/pair_modify.txt
View File

@ -15,11 +15,13 @@ pair_modify keyword values ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l
{pair} values = sub-style N {special} which wt1 wt2 wt3
or sub-style N {compute/tally} flag
sub-style = sub-style of "pair hybrid"_pair_hybrid.html
N = which instance of sub-style (only if sub-style is used multiple times)
{special} which wt1 wt2 wt3 = override {special_bonds} settings (optional)
which = {lj/coul} or {lj} or {coul}
w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
{special} which wt1 wt2 wt3 = override {special_bonds} settings (optional)
which = {lj/coul} or {lj} or {coul}
w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
{compute/tally} flag = {yes} or {no}
{mix} value = {geometric} or {arithmetic} or {sixthpower}
{shift} value = {yes} or {no}
{table} value = N
@ -40,6 +42,7 @@ pair_modify shift yes mix geometric
pair_modify tail yes
pair_modify table 12
pair_modify pair lj/cut compute no
pair_modify pair tersoff compute/tally no
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0 :pre
[Description:]
@ -60,9 +63,12 @@ keywords will be applied to. Note that if the {pair} keyword is not
used, and the pair style is {hybrid} or {hybrid/overlay}, then all the
specified keywords will be applied to all sub-styles.
The {special} keyword can only be used in conjunction with the {pair}
keyword and must directly follow it. It allows to override the
The {special} and {compute/tally} keywords can [only] be used in
conjunction with the {pair} keyword and must directly follow it.
{special} allows to override the
"special_bonds"_special_bonds.html settings for the specified sub-style.
{compute/tally} allows to disable or enable registering
"compute */tally"_compute_tally.html computes for a given sub-style.
More details are given below.
The {mix} keyword affects pair coefficients for interactions between
@ -231,6 +237,14 @@ setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
usually a sufficient workaround in this case without causing a
significant error.
The {compute/tally} keyword takes exactly 1 argument ({no} or {yes}),
and allows to selectively disable or enable processing of the various
"compute */tally"_compute_tally.html styles for a given
"pair hybrid or hybrid/overlay"_pair_hybrid.html sub-style.
NOTE: Any "pair_modify pair compute/tally" command must be issued
[before] the corresponding compute style is defined.
:line
[Restrictions:] none
@ -240,8 +254,9 @@ conflicting options. You cannot use {tail} yes with 2d simulations.
[Related commands:]
"pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html,
"thermo_style"_thermo_style.html
"pair_style"_pair_style.html, "pair_style hybrid"_pair_hybrid.html,
pair_coeff"_pair_coeff.html, "thermo_style"_thermo_style.html,
"compute */tally"_compute_tally.html
[Default:]

2
doc/src/pair_srp.txt
View File

@ -150,6 +150,8 @@ hybrid"_pair_hybrid.html.
This pair style requires the "newton"_newton.html command to be {on}
for non-bonded interactions.
This pair style is not compatible with "rigid body integrators"_fix_rigid.html
[Related commands:]
"pair_style hybrid"_pair_hybrid.html, "pair_coeff"_pair_coeff.html,

2
doc/src/python.txt
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@ -310,7 +310,7 @@ which corresponds to SELF in the python command. The first line of
the function imports the Python module lammps.py in the python dir of
the distribution. The second line creates a Python object "lmp" which
wraps the instance of LAMMPS that called the function. The
"ptr=lmpptr" argument is what makes that happen. The thrid line
"ptr=lmpptr" argument is what makes that happen. The third line
invokes the command() function in the LAMMPS library interface. It
takes a single string argument which is a LAMMPS input script command
for LAMMPS to execute, the same as if it appeared in your input

8
lib/molfile/Makefile.lammps
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@ -6,6 +6,9 @@
# When you build LAMMPS with the USER-MOLFILE package installed, it will
# use the 3 settings in this file. They should be set as follows.
#
# The molfile_SYSINC setting is to point to the folder with the VMD
# plugin headers. By default it points to bundled headers in this folder
#
# The molfile_SYSLIB setting is for a system dynamic loading library
# that will be used to load the molfile plugins. It contains functions
# like dlopen(), dlsym() and so on for dynamic linking of executable
@ -24,7 +27,10 @@
# Settings that the LAMMPS build will import when this package is installed
molfile_SYSINC =
# change this to -I/path/to/your/lib/vmd/plugins/include if the bundled
# header files are incompatible with your VMD plugsins
molfile_SYSINC =-I../../lib/molfile
#
ifneq ($(LIBOBJDIR),/Obj_mingw32)
ifneq ($(LIBOBJDIR),/Obj_mingw64)
ifneq ($(LIBOBJDIR),/Obj_mingw32-mpi)

27
lib/molfile/README
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@ -6,17 +6,30 @@ and write_dump commands in a LAMMPS input script.
More information about the VMD molfile plugins can be found at
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
More specifically, to be able to dynamically load and execute the
plugins from inside LAMMPS, you need to link with a system library
containing functions like dlopen(), dlsym() and so on for dynamic
linking of executable code into an executable. This library is
defined by setting the molfile_SYSLIB variable in the Makefile.lammps
file in this dir.
NOTE: while the programming interface (API) of the VMD molfile plugins
is backward compatible (i.e. you can expect to be able to compile this
package for plugins from newer VMD packages), the binary interface
(ABI) is not. So it is necessary to compile this package with the
VMD molfile plugin header files (vmdplugin.h and molfile_plugin.h)
matching VMD installation that the (binary) plugin files are taken from.
These header files can be found inside the VMD installation tree under
"plugins/include". For convenience, this package includes a set of
header files that is compatible with VMD 1.9.3 (the current version
in April 2017). You need to adjust the molfile_SYSINC variable in the
Makefile.lammps file in this directory, in case you want to use VMD
molfile plugins from a different version. The interface is compatible
with plugins starting from VMD version 1.8.4.
In order to be able to dynamically load and execute the plugins from
inside LAMMPS, you need to link with a system library containing functions
like dlopen(), dlsym() and so on for dynamic linking of executable code
into an executable. This library is defined by setting the molfile_SYSLIB
variable in the Makefile.lammps file in this dir.
For Linux and most current unix-like operating systems, this can be
kept at the default setting of "-ldl" (on some platforms this library
is called "-ldld"). For compilation on Windows, a slightly different
mechanism is used that is part of the Windows programming environment
and this library is not needed.
and this kind of library is not needed.
See the header of Makefile.lammps for more info.

135
src/USER-MOLFILE/molfile_plugin.h → lib/molfile/molfile_plugin.h
View File

@ -11,7 +11,7 @@
*
* $RCSfile: molfile_plugin.h,v $
* $Author: johns $ $Locker: $ $State: Exp $
* $Revision: 1.103 $ $Date: 2011/03/05 03:56:11 $
* $Revision: 1.108 $ $Date: 2016/02/26 03:17:01 $
*
***************************************************************************/
@ -60,6 +60,21 @@ typedef ssize_t molfile_ssize_t; /**< for frame counts */
#define MOLFILE_MAXWAVEPERTS 25 /**< maximum number of wavefunctions
* per timestep */
/**
* Hard-coded direct-I/O page size constants for use by both VMD
* and the plugins that want to use direct, unbuffered I/O for high
* performance with SSDs etc. We use two constants to define the
* range of hardware page sizes that we can support, so that we can
* add support for larger 8KB or 16KB page sizes in the future
* as they become more prevalent in high-end storage systems.
*
* At present, VMD uses a hard-coded 4KB page size to reduce memory
* fragmentation, but these constants will make it easier to enable the
* use of larger page sizes in the future if it becomes necessary.
*/
#define MOLFILE_DIRECTIO_MIN_BLOCK_SIZE 4096
#define MOLFILE_DIRECTIO_MAX_BLOCK_SIZE 4096
/**
* File level comments, origin information, and annotations.
@ -96,8 +111,17 @@ typedef struct {
char resname[8]; /**< required residue name string */
int resid; /**< required integer residue ID */
char segid[8]; /**< required segment name string, or "" */
#if 0 && vmdplugin_ABIVERSION > 17
/* The new PDB file formats allows for much larger structures, */
/* which can therefore require longer chain ID strings. The */
/* new PDBx/mmCIF file formats do not have length limits on */
/* fields, so PDB chains could be arbitrarily long strings */
/* in such files. At present, we know we need at least 3-char */
/* chains for existing PDBx/mmCIF files. */
char chain[4]; /**< required chain name, or "" */
#else
char chain[2]; /**< required chain name, or "" */
#endif
/* rest are optional; use optflags to specify what's present */
char altloc[2]; /**< optional PDB alternate location code */
char insertion[2]; /**< optional PDB insertion code */
@ -107,6 +131,23 @@ typedef struct {
float charge; /**< optional charge value */
float radius; /**< optional radius value */
int atomicnumber; /**< optional element atomic number */
#if 0
char complex[16];
char assembly[16];
int qmregion;
int qmregionlink;
int qmlayer;
int qmlayerlink;
int qmfrag;
int qmfraglink;
string qmecp;
int qmadapt;
int qmect; /**< boolean */
int qmparam;
int autoparam;
#endif
#if defined(DESRES_CTNUMBER)
int ctnumber; /**< mae ct block, 0-based, including meta */
#endif
@ -140,23 +181,19 @@ typedef struct {
#define MOLFILE_QMTS_SCFITER 0x0002
/*@}*/
#if vmdplugin_ABIVERSION > 10
typedef struct molfile_timestep_metadata {
unsigned int count; /**< total # timesteps; -1 if unknown */
unsigned int avg_bytes_per_timestep; /** bytes per timestep */
int has_velocities; /**< if timesteps have velocities */
} molfile_timestep_metadata_t;
#endif
/*
* Per-timestep atom coordinates and periodic cell information
*/
typedef struct {
float *coords; /**< coordinates of all atoms, arranged xyzxyzxyz */
#if vmdplugin_ABIVERSION > 10
float *velocities; /**< space for velocities of all atoms; same layout */
/**< NULL unless has_velocities is set */
#endif
/*@{*/
/**
@ -169,9 +206,7 @@ typedef struct {
float A, B, C, alpha, beta, gamma;
/*@}*/
#if vmdplugin_ABIVERSION > 10
double physical_time; /**< physical time point associated with this frame */
#endif
#if defined(DESRES_READ_TIMESTEP2)
/* HACK to support generic trajectory information */
@ -213,14 +248,33 @@ typedef struct {
* physical size of the box, this is the number of voxels in each
* direction, independent of the shape of the volume set.
*/
int xsize; /**< number of grid cells along the X axis */
int ysize; /**< number of grid cells along the Y axis */
int zsize; /**< number of grid cells along the Z axis */
int xsize; /**< number of grid cells along the X axis */
int ysize; /**< number of grid cells along the Y axis */
int zsize; /**< number of grid cells along the Z axis */
int has_color; /**< flag indicating presence of voxel color data */
#if vmdplugin_ABIVERSION > 16
int has_scalar; /**< flag indicating presence of scalar volume */
int has_gradient; /**< flag indicating presence of vector volume */
int has_variance; /**< flag indicating presence of variance map */
#endif
int has_color; /**< flag indicating presence of voxel color data */
} molfile_volumetric_t;
#if vmdplugin_ABIVERSION > 16
/**
* Volumetric dataset read/write structure with both flag/parameter sets
* and VMD-allocated pointers for fields to be used by the plugin.
*/
typedef struct {
int setidx; /**< volumetric dataset index to load/save */
float *scalar; /**< scalar density/potential field data */
float *gradient; /**< gradient vector field */
float *variance; /**< variance map indicating signal/noise */
float *rgb3f; /**< RGB floating point color texture map */
unsigned char *rgb3u; /**< RGB unsigned byte color texture map */
} molfile_volumetric_readwrite_t;
#endif
/**************************************************************
@ -231,9 +285,6 @@ typedef struct {
**************************************************************
**************************************************************/
#if vmdplugin_ABIVERSION > 9
/* macros for the convergence status of a QM calculation. */
#define MOLFILE_QMSTATUS_UNKNOWN -1 /* don't know yet */
#define MOLFILE_QMSTATUS_OPT_CONV 0 /* optimization converged */
@ -485,8 +536,6 @@ typedef struct {
} molfile_qm_timestep_t;
#endif
/**************************************************************
**************************************************************/
@ -609,12 +658,8 @@ typedef struct {
* This function can be called only after read_structure().
* Return MOLFILE_SUCCESS if no errors occur.
*/
#if vmdplugin_ABIVERSION > 14
int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
int **bondtype, int *nbondtypes, char ***bondtypename);
#else
int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder);
#endif
/**
* XXX this function will be augmented and possibly superceded by a
@ -684,6 +729,9 @@ typedef struct {
*/
int (* read_volumetric_data)(void *, int set, float *datablock,
float *colorblock);
#if vmdplugin_ABIVERSION > 16
int (* read_volumetric_data_ex)(void *, molfile_volumetric_readwrite_t *v);
#endif
/**
* Read raw graphics data stored in this file. Return the number of data
@ -723,14 +771,9 @@ typedef struct {
* bondtypenames can only be used of bondtypes is also given.
* Return MOLFILE_SUCCESS if no errors occur.
*/
#if vmdplugin_ABIVERSION > 14
int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
int *bondtype, int nbondtypes, char **bondtypename);
#else
int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder);
#endif
#if vmdplugin_ABIVERSION > 9
/**
* Write the specified volumetric data set into the space pointed to by
* datablock. The * allocated for the datablock must be equal to
@ -740,8 +783,11 @@ typedef struct {
*/
int (* write_volumetric_data)(void *, molfile_volumetric_t *metadata,
float *datablock, float *colorblock);
#if vmdplugin_ABIVERSION > 16
int (* write_volumetric_data_ex)(void *, molfile_volumetric_t *metadata,
molfile_volumetric_readwrite_t *v);
#endif
#if vmdplugin_ABIVERSION > 15
/**
* Read in Angles, Dihedrals, Impropers, and Cross Terms and optionally types.
* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
@ -764,33 +810,6 @@ typedef struct {
const int *impropers, const int *impropertypes, int numimpropertypes,
const char **impropertypenames, int numcterms, const int *cterms,
int ctermcols, int ctermrows);
#else
/**
* Read in Angles, Dihedrals, Impropers, and Cross Terms
* Forces are in Kcal/mol
* (Cross terms pertain to the CHARMM/NAMD CMAP feature, forces are given
* as a 2-D matrix)
*/
int (* read_angles)(void *,
int *numangles, int **angles, double **angleforces,
int *numdihedrals, int **dihedrals, double **dihedralforces,
int *numimpropers, int **impropers, double **improperforces,
int *numcterms, int **cterms,
int *ctermcols, int *ctermrows, double **ctermforces);
/**
* Write out Angles, Dihedrals, Impropers, and Cross Terms
* Forces are in Kcal/mol
* (Cross terms pertain to the CHARMM/NAMD CMAP feature, forces are given
* as a 2-D matrix)
*/
int (* write_angles)(void *,
int numangles, const int *angles, const double *angleforces,
int numdihedrals, const int *dihedrals, const double *dihedralforces,
int numimpropers, const int *impropers, const double *improperforces,
int numcterms, const int *cterms,
int ctermcols, int ctermrows, const double *ctermforces);
#endif
/**
@ -839,14 +858,9 @@ typedef struct {
*/
int (* read_timestep)(void *, int natoms, molfile_timestep_t *,
molfile_qm_metadata_t *, molfile_qm_timestep_t *);
#endif
#if vmdplugin_ABIVERSION > 10
int (* read_timestep_metadata)(void *, molfile_timestep_metadata_t *);
#endif
#if vmdplugin_ABIVERSION > 11
int (* read_qm_timestep_metadata)(void *, molfile_qm_timestep_metadata_t *);
#endif
#if defined(DESRES_READ_TIMESTEP2)
/**
@ -864,7 +878,6 @@ typedef struct {
double * times );
#endif
#if vmdplugin_ABIVERSION > 13
/**
* Console output, READ-ONLY function pointer.
* Function pointer that plugins can use for printing to the host
@ -883,8 +896,8 @@ typedef struct {
* application-provided services
*/
int (* cons_fputs)(const int, const char*);
#endif
} molfile_plugin_t;
#endif

4
src/USER-MOLFILE/vmdplugin.h → lib/molfile/vmdplugin.h
View File

@ -11,7 +11,7 @@
*
* $RCSfile: vmdplugin.h,v $
* $Author: johns $ $Locker: $ $State: Exp $
* $Revision: 1.32 $ $Date: 2009/02/24 05:12:35 $
* $Revision: 1.33 $ $Date: 2015/10/29 05:10:54 $
*
***************************************************************************/
@ -144,7 +144,7 @@ typedef struct {
/**
* Use this macro to initialize the abiversion member of each plugin
*/
#define vmdplugin_ABIVERSION 16
#define vmdplugin_ABIVERSION 17
/*@{*/
/** Use this macro to indicate a plugin's thread-safety at registration time */

12
src/.gitignore vendored
View File

@ -47,8 +47,6 @@
/dump_molfile.h
/molfile_interface.cpp
/molfile_interface.h
/molfile_plugin.h
/vmdplugin.h
/type_detector.h
/intel_buffers.cpp
@ -76,8 +74,8 @@
/pair_awpmd_cut.cpp
/pair_awpmd_cut.h
/dihedral_charmmfsh.cpp
/dihedral_charmmfsh.h
/dihedral_charmmfsw.cpp
/dihedral_charmmfsw.h
/pair_lj_charmmfsw_coul_charmmfsh.cpp
/pair_lj_charmmfsw_coul_charmmfsh.h
/pair_lj_charmmfsw_coul_long.cpp
@ -163,6 +161,8 @@
/bond_nonlinear.h
/bond_oxdna_fene.cpp
/bond_oxdna_fene.h
/bond_oxdna2_fene.cpp
/bond_oxdna2_fene.h
/bond_quartic.cpp
/bond_quartic.h
/bond_table.cpp
@ -770,6 +770,8 @@
/pair_nm_cut_coul_long.h
/pair_oxdna_*.cpp
/pair_oxdna_*.h
/pair_oxdna2_*.cpp
/pair_oxdna2_*.h
/mf_oxdna.h
/pair_peri_eps.cpp
/pair_peri_eps.h
@ -848,6 +850,8 @@
/prd.h
/python.cpp
/python.h
/python_impl.cpp
/python_impl.h
/reader_molfile.cpp
/reader_molfile.h
/reaxc_allocate.cpp

7
src/KSPACE/ewald_disp.cpp
View File

@ -138,13 +138,14 @@ void EwaldDisp::init()
nsums += n[k];
}
if (!gewaldflag) g_ewald = 0.0;
if (!gewaldflag) g_ewald = g_ewald_6 = 1.0;
pair->init(); // so B is defined
init_coeffs();
init_coeff_sums();
if (function[0]) qsum_qsq();
else qsqsum = qsum = 0.0;
natoms_original = atom->natoms;
if (!gewaldflag) g_ewald = g_ewald_6 = 0.0;
// turn off coulombic if no charge
@ -218,8 +219,8 @@ void EwaldDisp::init()
}
if (!comm->me) {
if (screen) fprintf(screen, " G vector = %g\n", g_ewald);
if (logfile) fprintf(logfile, " G vector = %g\n", g_ewald);
if (screen) fprintf(screen, " G vector = %g, accuracy = %g\n", g_ewald,accuracy);
if (logfile) fprintf(logfile, " G vector = %g accuracy = %g\n", g_ewald,accuracy);
}
g_ewald_6 = g_ewald;

12
src/KSPACE/pppm_disp.cpp
View File

@ -380,6 +380,12 @@ void PPPMDisp::init()
alpha = qdist / (cos(0.5*theta) * blen);
}
//if g_ewald and g_ewald_6 have not been specified, set some initial value
// to avoid problems when calculating the energies!
if (!gewaldflag) g_ewald = 1;
if (!gewaldflag_6) g_ewald_6 = 1;
// initialize the pair style to get the coefficients
neighrequest_flag = 0;
@ -387,12 +393,6 @@ void PPPMDisp::init()
neighrequest_flag = 1;
init_coeffs();
//if g_ewald and g_ewald_6 have not been specified, set some initial value
// to avoid problems when calculating the energies!
if (!gewaldflag) g_ewald = 1;
if (!gewaldflag_6) g_ewald_6 = 1;
// set accuracy (force units) from accuracy_relative or accuracy_absolute
if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute;

6
src/Purge.list
View File

@ -16,6 +16,12 @@ style_region.h
style_neigh_bin.h
style_neigh_pair.h
style_neigh_stencil.h
# deleted on 19 April 2017
vmdplugin.h
molfile_plugin.h
# deleted on 13 April 2017
dihedral_charmmfsh.cpp
dihedral_charmmfsh.h
# deleted on ## XXX 2016
accelerator_intel.h
neigh_bond.cpp

2
src/QEQ/fix_qeq_point.cpp
View File

@ -58,7 +58,7 @@ void FixQEqPoint::init()
neighbor->requests[irequest]->full = 1;
int ntypes = atom->ntypes;
memory->create(shld,ntypes+1,ntypes+1,"qeq:shileding");
memory->create(shld,ntypes+1,ntypes+1,"qeq:shielding");
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;

7
src/USER-MISC/fix_srp.cpp
View File

@ -101,6 +101,13 @@ void FixSRP::init()
if (force->pair_match("hybrid",1) == NULL)
error->all(FLERR,"Cannot use pair srp without pair_style hybrid");
int has_rigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (strncmp(modify->fix[i]->style,"rigid",5) == 0) ++has_rigid;
if (has_rigid > 0)
error->all(FLERR,"Pair srp is not compatible with rigid fixes.");
if ((bptype < 1) || (bptype > atom->ntypes))
error->all(FLERR,"Illegal bond particle type");

2
src/USER-MISC/improper_ring.cpp
View File

@ -204,7 +204,7 @@ void ImproperRing::compute(int eflag, int vflag)
cfact2 = ckjji / ckjkj;
cfact3 = ckjji / cjiji;
/* Calculate the force acted on the thrid atom of the angle. */
/* Calculate the force acted on the third atom of the angle. */
fkx = cfact2 * bvec2x[icomb] - bvec1x[icomb];
fky = cfact2 * bvec2y[icomb] - bvec1y[icomb];
fkz = cfact2 * bvec2z[icomb] - bvec1z[icomb];

17
src/USER-MOLFILE/README
View File

@ -2,8 +2,8 @@ This package provides a C++ interface class to the VMD molfile
plugins, http://www.ks.uiuc.edu/Research/vmd/plugins/molfile, and a
set of LAMMPS classes that use this interface.
Molfile plugins provide a consistent programming interface to read and
write file formats commonly used in molecular simulations. This
Molfile plugins provide a consistent programming interface to read
and write file formats commonly used in molecular simulations. This
package only provides the interface code, not the plugins; these can
be taken as precompiled binaries directly from a VMD installation that
matches the platform of your LAMMPS executable. Using the plugin
@ -18,18 +18,5 @@ LAMMPS, you need to link with an appropriate system library, which
is done using the settings in lib/molfile/Makefile.lammps. See
that file and the lib/molfile/README file for more details.
NOTE: while the programming interface (API) to the molfile plugins is
backward compatible (i.e. you can expect to be able to compile this
package for plugins from newer VMD packages), the binary interface
(ABI) is not. So it is necessary to compile this package with the
molfile plugin header files (vmdplugin.h and molfile_plugin.h) taken
from the _same_ VMD installation that the (binary) plugin files are
taken from. These header files can be found inside the VMD
installation tree under: "plugins/include".
For convenience, this package includes a set of header files that is
compatible with VMD 1.9 and 1.9.1 (the current version in June 2012)
and should be compilable with VMD versions back to about version 1.8.4
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.

2
src/USER-OMP/improper_ring_omp.cpp
View File

@ -206,7 +206,7 @@ void ImproperRingOMP::eval(int nfrom, int nto, ThrData * const thr)
cfact2 = ckjji / ckjkj;
cfact3 = ckjji / cjiji;
/* Calculate the force acted on the thrid atom of the angle. */
/* Calculate the force acted on the third atom of the angle. */
fkx = cfact2 * bvec2x[icomb] - bvec1x[icomb];
fky = cfact2 * bvec2y[icomb] - bvec1y[icomb];
fkz = cfact2 * bvec2z[icomb] - bvec1z[icomb];

2
src/USER-REAXC/fix_qeq_reax.cpp
View File

@ -375,7 +375,7 @@ void FixQEqReax::init_shielding()
ntypes = atom->ntypes;
if (shld == NULL)
memory->create(shld,ntypes+1,ntypes+1,"qeq:shileding");
memory->create(shld,ntypes+1,ntypes+1,"qeq:shielding");
for( i = 1; i <= ntypes; ++i )
for( j = 1; j <= ntypes; ++j )

4
src/USER-TALLY/compute_force_tally.cpp
View File

@ -65,12 +65,12 @@ ComputeForceTally::~ComputeForceTally()
void ComputeForceTally::init()
{
if (force->pair == NULL)
error->all(FLERR,"Trying to use compute force/tally with no pair style");
error->all(FLERR,"Trying to use compute force/tally without pair style");
else
force->pair->add_tally_callback(this);
if (force->pair->single_enable == 0 || force->pair->manybody_flag)
error->all(FLERR,"Compute force/tally used with incompatible pair style.");
error->warning(FLERR,"Compute force/tally used with incompatible pair style");
if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
|| force->improper || force->kspace))

4
src/USER-TALLY/compute_heat_flux_tally.cpp
View File

@ -64,12 +64,12 @@ ComputeHeatFluxTally::~ComputeHeatFluxTally()
void ComputeHeatFluxTally::init()
{
if (force->pair == NULL)
error->all(FLERR,"Trying to use compute heat/flux/tally with no pair style");
error->all(FLERR,"Trying to use compute heat/flux/tally without pair style");
else
force->pair->add_tally_callback(this);
if (force->pair->single_enable == 0 || force->pair->manybody_flag)
error->all(FLERR,"Compute heat/flux/tally used with incompatible pair style.");
error->warning(FLERR,"Compute heat/flux/tally used with incompatible pair style");
if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
|| force->improper || force->kspace))

6
src/USER-TALLY/compute_pe_mol_tally.cpp
View File

@ -59,15 +59,15 @@ ComputePEMolTally::~ComputePEMolTally()
void ComputePEMolTally::init()
{
if (force->pair == NULL)
error->all(FLERR,"Trying to use compute pe/mol/tally with no pair style");
error->all(FLERR,"Trying to use compute pe/mol/tally without pair style");
else
force->pair->add_tally_callback(this);
if (atom->molecule_flag == 0)
error->all(FLERR,"Compute pe/mol/tally requires molecule IDs.");
error->all(FLERR,"Compute pe/mol/tally requires molecule IDs");
if (force->pair->single_enable == 0 || force->pair->manybody_flag)
error->all(FLERR,"Compute pe/mol/tally used with incompatible pair style.");
error->warning(FLERR,"Compute pe/mol/tally used with incompatible pair style");
if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
|| force->improper || force->kspace))

4
src/USER-TALLY/compute_pe_tally.cpp
View File

@ -64,12 +64,12 @@ ComputePETally::~ComputePETally()
void ComputePETally::init()
{
if (force->pair == NULL)
error->all(FLERR,"Trying to use compute pe/tally with no pair style");
error->all(FLERR,"Trying to use compute pe/tally without a pair style");
else
force->pair->add_tally_callback(this);
if (force->pair->single_enable == 0 || force->pair->manybody_flag)
error->all(FLERR,"Compute pe/tally used with incompatible pair style.");
error->warning(FLERR,"Compute pe/tally used with incompatible pair style");
if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
|| force->improper || force->kspace))

4
src/USER-TALLY/compute_stress_tally.cpp
View File

@ -65,12 +65,12 @@ ComputeStressTally::~ComputeStressTally()
void ComputeStressTally::init()
{
if (force->pair == NULL)
error->all(FLERR,"Trying to use compute stress/tally with no pair style");
error->all(FLERR,"Trying to use compute stress/tally without pair style");
else
force->pair->add_tally_callback(this);
if (force->pair->single_enable == 0 || force->pair->manybody_flag)
error->all(FLERR,"Compute stress/tally used with incompatible pair style.");
error->warning(FLERR,"Compute stress/tally used with incompatible pair style");
if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
|| force->improper || force->kspace))

9
src/min.cpp
View File

@ -187,6 +187,8 @@ void Min::setup(int flag)
update->minimize_style);
if (flag) {
fprintf(screen," Unit style : %s\n", update->unit_style);
fprintf(screen," Current step : " BIGINT_FORMAT "\n",
update->ntimestep);
timer->print_timeout(screen);
}
}
@ -196,7 +198,12 @@ void Min::setup(int flag)
// cannot be done in init() b/c update init() is before modify init()
nextra_global = modify->min_dof();
if (nextra_global) fextra = new double[nextra_global];
if (nextra_global) {
fextra = new double[nextra_global];
if (comm->me == 0 && screen)
fprintf(screen,"WARNING: Energy due to %d extra global DOFs will"
" be included in minimizer energies\n",nextra_global);
}
// compute for potential energy

6
src/min.h
View File

@ -123,6 +123,12 @@ Minimization requires that neigh_modify settings be delay = 0, every =
changed them and will restore them to their original values after the
minimization.
W: Energy due to X extra global DOFs will be included in minimizer energies
When using fixes like box/relax, the potential energy used by the minimizer
is augmented by an additional energy provided by the fix. Thus the printed
converged energy may be different from the total potential energy.
E: Minimization could not find thermo_pe compute
This compute is created by the thermo command. It must have been

4
src/pair.h
View File

@ -194,8 +194,8 @@ class Pair : protected Pointers {
int num_tally_compute;
class Compute **list_tally_compute;
public:
void add_tally_callback(class Compute *);
void del_tally_callback(class Compute *);
virtual void add_tally_callback(class Compute *);
virtual void del_tally_callback(class Compute *);
protected:
int instance_me; // which Pair class instantiation I am

37
src/pair_hybrid.cpp
View File

@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
PairHybrid::PairHybrid(LAMMPS *lmp) : Pair(lmp),
styles(NULL), keywords(NULL), multiple(NULL), nmap(NULL),
map(NULL), special_lj(NULL), special_coul(NULL)
map(NULL), special_lj(NULL), special_coul(NULL), compute_tally(NULL)
{
nstyles = 0;
@ -62,6 +62,7 @@ PairHybrid::~PairHybrid()
delete [] special_lj;
delete [] special_coul;
delete [] compute_tally;
delete [] svector;
@ -169,6 +170,23 @@ void PairHybrid::compute(int eflag, int vflag)
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairHybrid::add_tally_callback(Compute *ptr)
{
for (int m = 0; m < nstyles; m++)
if (compute_tally[m]) styles[m]->add_tally_callback(ptr);
}
/* ---------------------------------------------------------------------- */
void PairHybrid::del_tally_callback(Compute *ptr)
{
for (int m = 0; m < nstyles; m++)
if (compute_tally[m]) styles[m]->del_tally_callback(ptr);
}
/* ---------------------------------------------------------------------- */
void PairHybrid::compute_inner()
@ -253,6 +271,8 @@ void PairHybrid::settings(int narg, char **arg)
special_lj = new double*[narg];
special_coul = new double*[narg];
compute_tally = new int[narg];
// allocate each sub-style
// allocate uses suffix, but don't store suffix version in keywords,
// else syntax in coeff() will not match
@ -272,6 +292,7 @@ void PairHybrid::settings(int narg, char **arg)
styles[nstyles] = force->new_pair(arg[iarg],1,dummy);
force->store_style(keywords[nstyles],arg[iarg],0);
special_lj[nstyles] = special_coul[nstyles] = NULL;
compute_tally[nstyles] = 1;
jarg = iarg + 1;
while (jarg < narg && !force->pair_map->count(arg[jarg])) jarg++;
@ -782,6 +803,20 @@ void PairHybrid::modify_params(int narg, char **arg)
iarg += 5;
}
// if 2nd keyword (after pair) is compute/tally:
// set flag to register USER-TALLY computes accordingly
if (iarg < narg && strcmp(arg[iarg],"compute/tally") == 0) {
if (narg < iarg+2)
error->all(FLERR,"Illegal pair_modify compute/tally command");
if (strcmp(arg[iarg+1],"yes") == 0) {
compute_tally[m] = 1;
} else if (strcmp(arg[iarg+1],"no") == 0) {
compute_tally[m] = 0;
} else error->all(FLERR,"Illegal pair_modify compute/tally command");
iarg += 2;
}
// apply the remaining keywords to the base pair style itself and the
// sub-style except for "pair" and "special".
// the former is important for some keywords like "tail" or "compute"

4
src/pair_hybrid.h
View File

@ -55,6 +55,9 @@ class PairHybrid : public Pair {
int check_ijtype(int, int, char *);
virtual void add_tally_callback(class Compute *);
virtual void del_tally_callback(class Compute *);
protected:
int nstyles; // # of sub-styles
Pair **styles; // list of Pair style classes
@ -69,6 +72,7 @@ class PairHybrid : public Pair {
int ***map; // list of sub-styles itype,jtype points to
double **special_lj; // list of per style LJ exclusion factors
double **special_coul; // list of per style Coulomb exclusion factors
int *compute_tally; // list of on/off flags for tally computes
void allocate();
void flags();

271
tools/msi2lmp/README
View File

@ -1,98 +1,50 @@
Axel Kohlmeyer is the current maintainer of the msi2lmp tool.
Please send any inquiries about msi2lmp to the lammps-users mailing list.
06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>
msi2lmp.exe
Improved whitespace handling in parsing topology and force field
files to avoid bogus warnings about type name truncation.
This code has several known limitations listed below under "LIMITATIONS"
(and possibly some unknown ones, too) and is no longer under active
development. Only the occasional bugfix is applied.
24 Oct 2015 Axel Kohlmeyer <akohlmey@gmail.com>
Please send any inquiries about msi2lmp to the lammps-users
mailing list and not to individual people.
Added check to make certain that force field files
are consistent with the notation of non-bonded parameters
that the msi2lmp code expects. For Class 1 and OPLS-AA
the A-B notation with geometric mixing is expected and for
Class 2 the r-eps notation with sixthpower mixing.
------------------------------------------------------------------------
11 Sep 2014 Axel Kohlmeyer <akohlmey@gmail.com>
OVERVIEW
Refactored ReadMdfFile.c so it more consistently honors
the MAX_NAME and MAX_STRING string length defines and
potentially handles inputs with long names better.
This is the third version of a program that generates a LAMMPS data file
based on the information in MSI .car (atom coordinates), .mdf (molecular
topology) and .frc (forcefield) files. The .car and .mdf files are
specific to a molecular system while the .frc file is specific to a
forcefield version. The only coherency needed between .frc and
.car/.mdf files are the atom types.
27 May 2014 Axel Kohlmeyer <akohlmey@gmail.com>
The first version was written by Steve Lustig at Dupont, but required
using Discover to derive internal coordinates and forcefield parameters
Added TopoTools style type hints as comments to all Mass, PairCoeff,
BondCoeff, AngleCoeff, DihedralCoeff, ImproperCoeff entries.
This should make it easier to identify force field entries with
the structure and force field map in the data file later.
The second version was written by Michael Peachey while an intern in the
Cray Chemistry Applications Group managed by John Carpenter. This
version derived internal coordinates from the mdf file and looked up
parameters in the frc file thus eliminating the need for Discover.
06 Mar 2014 Axel Kohlmeyer <akohlmey@gmail.com>
The third version was written by John Carpenter to optimize the
performance of the program for large molecular systems (the original
code for deriving atom numbers was quadratic in time) and to make the
program fully dynamic. The second version used fixed dimension arrays
for the internal coordinates.
Fixed a bug in handling of triclinic cells, where the matrices to
convert to and from fractional coordinates were incorrectly built.
The third version was revised in Fall 2011 by Stephanie Teich-McGoldrick
to add support non-orthogonal cells.
26 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
The next revision was started in Summer/Fall 2013 by Axel Kohlmeyer to
improve portability to Windows compilers, clean up command line parsing
and improve compatibility with the then current LAMMPS versions. This
revision removes compatibility with the obsolete LAMMPS version written
in Fortran 90.
Implemented writing out force field style hints in generated data
files for improved consistency checking when reading those files.
Also added writing out CGCMM style comments to identify atom types.
INSTALLATION & USAGE
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
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
input provided by jeff greathouse.
18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Added support for writing out image flags
Improved accuracy of atom masses
Added flag for shifting the entire system
Fixed some minor logic bugs and prepared
for supporting other force fields and morse style bonds.
12 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Fixed the bug that caused improper coefficients to be wrong
Cleaned up the handling of box parameters and center the box
by default around the system/molecule. Added a flag to make
this step optional and center the box around the origin instead.
Added a regression test script with examples.
1 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Cleanup and improved port to windows.
Removed some more static string limits.
Added print level 3 for additional output.
Make code stop at missing force field parameters
and added -i flag to override this.
Safer argument checking.
Provide short versions for all flags.
23 Sep 2011
added support for triclinic boxes
see msi2lmp/TriclinicModification.pdf doc for details
-----------------------------
msi2lmp V3.6 4/10/2005
This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
program to produce a LAMMPS data file.
1. Building msi2lmp
@ -178,50 +130,111 @@ see msi2lmp/TriclinicModification.pdf doc for details
-- the LAMMPS data file is written to <ROOTNAME>.data
protocol and error information is written to the screen.
****************************************************************
*
* msi2lmp
*
* This is the third version of a program that generates a LAMMPS
* data file based on the information in MSI .car (atom
* coordinates), .mdf (molecular topology) and .frc (forcefield)
* files. The .car and .mdf files are specific to a molecular
* system while the .frc file is specific to a forcefield version.
* The only coherency needed between .frc and .car/.mdf files are
* the atom types.
*
* The first version was written by Steve Lustig at Dupont, but
* required using Discover to derive internal coordinates and
* forcefield parameters
*
* The second version was written by Michael Peachey while an
* intern in the Cray Chemistry Applications Group managed
* by John Carpenter. This version derived internal coordinates
* from the mdf file and looked up parameters in the frc file
* thus eliminating the need for Discover.
*
* The third version was written by John Carpenter to optimize
* the performance of the program for large molecular systems
* (the original code for deriving atom numbers was quadratic in time)
* and to make the program fully dynamic. The second version used
* fixed dimension arrays for the internal coordinates.
*
* The current maintainer is only reluctantly doing so because John Mayo no longer
* needs this code.
*
* V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
* systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
* for number_of_dihedrals, etc. could be unpredictable in these systems.
*
* V3.3 was generated in response to a strange error reading a MDF file generated by
* Accelys' Materials Studio GUI. Simply rewriting the input part of ReadMdfFile.c
* seems to have fixed the problem.
*
* V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car and .mdf files
* written by Accelys' Materials Studio GUI.
*
* V3.6 outputs to LAMMPS 2005 (C++ version).
*
* Contact: Kelly L. Anderson, kelly.anderson@cantab.net
*
* April 2005
------------------------------------------------------------------------
LIMITATIONS
msi2lmp has the following known limitations:
- there is no support to select morse bonds over harmonic bonds
- there is no support for auto-equivalences to supplement fully
parameterized interactions with heuristic ones
- there is no support for bond increments
------------------------------------------------------------------------
CHANGELOG
06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>
Improved whitespace handling in parsing topology and force field
files to avoid bogus warnings about type name truncation.
24 Oct 2015 Axel Kohlmeyer <akohlmey@gmail.com>
Added check to make certain that force field files are consistent with
the notation of non-bonded parameters that the msi2lmp code expects.
For Class 1 and OPLS-AA the A-B notation with geometric mixing is
expected and for Class 2 the r-eps notation with sixthpower mixing.
11 Sep 2014 Axel Kohlmeyer <akohlmey@gmail.com>
Refactored ReadMdfFile.c so it more consistently honors the MAX_NAME
and MAX_STRING string length defines and potentially handles inputs
with long names better.
27 May 2014 Axel Kohlmeyer <akohlmey@gmail.com>
Added TopoTools style type hints as comments to all Mass, PairCoeff,
BondCoeff, AngleCoeff, DihedralCoeff, ImproperCoeff entries.
This should make it easier to identify force field entries with
the structure and force field map in the data file later.
06 Mar 2014 Axel Kohlmeyer <akohlmey@gmail.com>
Fixed a bug in handling of triclinic cells, where the matrices to
convert to and from fractional coordinates were incorrectly built.
26 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Implemented writing out force field style hints in generated data
files for improved consistency checking when reading those files.
Also added writing out CGCMM style comments to identify atom types.
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 input provided
by jeff greathouse.
18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Added support for writing out image flags. Improved accuracy of atom
masses. Added flag for shifting the entire system. Fixed some minor
logic bugs and prepared for supporting other force fields and morse
style bonds.
12 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Fixed the bug that caused improper coefficients to be wrong. Cleaned up
the handling of box parameters and center the box by default around the
system/molecule. Added a flag to make this step optional and center the
box around the origin instead. Added a regression test script with
examples.
1 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Cleanup and improved port to windows. Removed some more static string
limits. Added print level 3 for additional output. Make code stop at
missing force field parameters and added -i flag to override this.
Safer argument checking. Provide short versions for all flags.
23 Sep 2011
added support for triclinic boxes
V3.6 outputs to LAMMPS 2005 (C++ version).
Contact: Kelly L. Anderson, kelly.anderson@cantab.net
V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car
and .mdf files written by Accelys' Materials Studio GUI. April 2005
V3.3 was generated in response to a strange error reading a MDF file
generated by Accelys' Materials Studio GUI. Simply rewriting the input
part of ReadMdfFile.c seems to have fixed the problem.
V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
for number_of_dihedrals, etc. could be unpredictable in these systems.
-----------------------------
msi2lmp v3.9.8 6/10/2016

2
tools/msi2lmp/src/GetParameters.c
View File

@ -136,7 +136,7 @@ void GetParameters()
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
bondtypes[i].params[0] = ff_bond.data[k].ff_param[1];
bondtypes[i].params[1] = ff_bond.data[k].ff_param[0];
}
}
if (forcefield & FF_TYPE_CLASS2) {
for (j=0; j < 4; j++)

2
tools/msi2lmp/src/InitializeItems.c
View File

@ -68,7 +68,7 @@ void InitializeItems(void)
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_tor.keyword,"#torsion_1");
ff_tor.number_of_parameters = 3;
}
}
if (forcefield & FF_TYPE_CLASS2) {
strcpy(ff_tor.keyword,"#torsion_3");

2
tools/msi2lmp/src/WriteDataFile.c
View File

@ -144,7 +144,7 @@ void WriteDataFile(char *nameroot)
else if (forcefield & FF_TYPE_CLASS2)
fputs(" # class2\n\n",DatF);
} else fputs("\n\n",DatF);
for (i=0; i < no_angle_types; i++) {
fprintf(DatF, " %3i", i+1);
for ( j = 0; j < m; j++)

7
tools/msi2lmp/src/msi2lmp.c
View File

@ -142,9 +142,6 @@
* and to make the program fully dynamic. The second version used
* fixed dimension arrays for the internal coordinates.
*
* John Carpenter can be contacted by sending email to
* jec374@earthlink.net
*
* November 2000
*/
@ -356,7 +353,7 @@ int main (int argc, char *argv[])
if (centerflag) puts(" Output is recentered around geometrical center");
if (hintflag) puts(" Output contains style flag hints");
else puts(" Style flag hints disabled");
printf(" System translated by: %g %g %g\n",shift[0],shift[1],shift[2]);
printf(" System translated by: %g %g %g\n",shift[0],shift[1],shift[2]);
}
n = 0;
@ -374,7 +371,7 @@ int main (int argc, char *argv[])
if (n == 0) {
if (iflag > 0) fputs(" WARNING",stderr);
else fputs(" Error ",stderr);
fputs("- forcefield name and class appear to be inconsistent\n\n",stderr);
if (iflag == 0) return 7;
}

4
tools/msi2lmp/src/msi2lmp.h
View File

@ -24,13 +24,13 @@
* and to make the program fully dynamic. The second version used
* fixed dimension arrays for the internal coordinates.
*
* The thrid version was revised in Fall 2011 by
* The third version was revised in Fall 2011 by
* Stephanie Teich-McGoldrick to add support non-orthogonal cells.
*
* The next revision was started in Summer/Fall 2013 by
* Axel Kohlmeyer to improve portability to Windows compilers,
* clean up command line parsing and improve compatibility with
* the then current LAMMPS versions. This revision removes
* the then current LAMMPS versions. This revision removes
* compatibility with the obsolete LAMMPS version written in Fortran 90.
*/