Merge branch 'start_dump_h5md' of git://github.com/pdebuyl/lammps into merge_hdf5_support
This commit is contained in:
Axel Kohlmeyer
138
doc/dump_h5md.html
Normal file
138
doc/dump_h5md.html
Normal file
@ -0,0 +1,138 @@
|
||||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>dump h5md command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>dump ID group-ID h5md N file.h5 args
|
||||
</PRE>
|
||||
<UL><LI>ID = user-assigned name for the dump
|
||||
|
||||
<LI>group-ID = ID of the group of atoms to be imaged
|
||||
|
||||
<LI>h5md = style of dump command (other styles <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I> are discussed on the <A HREF = "dump.html">dump</A> doc page)
|
||||
|
||||
<LI>N = dump every this many timesteps
|
||||
|
||||
<LI>file.h5 = name of file to write to
|
||||
|
||||
<LI>args = list of data elements to dump, with their dump "subintervals".
|
||||
At least one element must be given and image may only be present if
|
||||
position is specified first.
|
||||
|
||||
<PRE> position options
|
||||
image
|
||||
velocity options
|
||||
force options
|
||||
species options
|
||||
file_from ID: do not open a new file, re-use the already opened file from dump ID
|
||||
box value = <I>yes</I> or <I>no</I>
|
||||
create_group value = <I>yes</I> or <I>no</I>
|
||||
author value = quoted string
|
||||
</PRE>
|
||||
<P>For the elements <I>position</I>, <I>velocity</I>, <I>force</I> and <I>species</I>, one may specify
|
||||
a sub-interval to write the data only every N_element iterations of the dump
|
||||
(i.e. every N*N_element time steps). This is specified by the option
|
||||
</P>
|
||||
<PRE> every N_element
|
||||
</PRE>
|
||||
<P>that follows directly the element declaration.
|
||||
</P>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>dump h5md1 all h5md 100 dump_h5md.h5 position image
|
||||
dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
|
||||
</PRE>
|
||||
<PRE>dump h5md1 all h5md 100 dump_h5md.h5 velocity author "L. Ammps"
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Dump a snapshot of atom coordinates every N timesteps in the <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5</A>
|
||||
based <A HREF = "http://nongnu.org/h5md/">H5MD</A> file format <A HREF = "#h5md_cpc">(de Buyl et al.)</A>.
|
||||
HDF5 files are binary, portable and self-describing.
|
||||
This dump style will write only one file, on the root node.
|
||||
</P>
|
||||
<P>Several dumps may write to the same file, by using file_from and referring to a
|
||||
previously defined dump.
|
||||
Several groups may also be stored within the same file by defining several dumps.
|
||||
A dump that refers (via <I>file_from</I>) to an already open dump ID and that
|
||||
concerns another particle group must specify <I>create_group yes</I>.
|
||||
</P>
|
||||
|
||||
|
||||
<P>Each data element is written every N*N_element steps. For <I>image</I>, no
|
||||
subinterval is needed as it must be present at the same interval as <I>position</I>.
|
||||
<I>image</I> must be given after <I>position</I> in any case.
|
||||
The box information (edges in each dimension) is stored at the same interval
|
||||
than the <I>position</I> element, if present. Else it is stored every N steps.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
|
||||
on timesteps when neighbor lists are rebuilt, the coordinates of an
|
||||
atom written to a dump file may be slightly outside the simulation
|
||||
box.
|
||||
</P>
|
||||
<P><B>Use from write_dump:</B>
|
||||
</P>
|
||||
<P>It is possible to use this dump style with the <A HREF = "write_dump.html">write_dump</A> command.
|
||||
In this case, the subintervals must not be set at all.
|
||||
<I>write_dump</I> can be used either alone or in conjunction with <I>file_from</I> so that
|
||||
fixed-in-time data can be stored in the same file as time-dependent data.
|
||||
</P>
|
||||
<P>Typically, the <I>species</I> data is fixed. The following two commands store the
|
||||
position data every 100 timesteps, with the image data, and store once the
|
||||
species data in the same file.
|
||||
</P>
|
||||
<PRE>dump h5md1 all h5md 100 dump.h5 position image
|
||||
write_dump all h5md dump.h5 file_from h5md1 species
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<UL>
|
||||
|
||||
<LI>The number of atoms per snapshot cannot change with the h5md style.
|
||||
|
||||
<LI>The position data is stored wrapped (box boundaries not enforced, see note above).
|
||||
|
||||
<LI>Only orthogonal domains are currently supported. This is a limitation of the
|
||||
present package and not of H5MD itself.
|
||||
|
||||
|
||||
</UL>
|
||||
<P>The <I>h5md</I> dump style is part of the USER-H5MD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info. It also requires
|
||||
(i) building the ch5md library provided with LAMMPS (See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.) and
|
||||
(ii) having the <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5</A> library installed (C bindings are sufficient).
|
||||
The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library.
|
||||
</P>
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "undump.html">undump</A>
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "h5md_cpc"></A>
|
||||
|
||||
<P><B>(de Buyl et al.)</B> de Buyl, Colberg and Hofling, H5MD: A structured, efficient,
|
||||
and portable file format for molecular data, Comp. Phys. Comm. 185(6),
|
||||
1546-1553 (2014) - <A HREF = "http://arxiv.org/abs/1308.6382/">[arXiv:1308.6382]</A>.
|
||||
</P>
|
||||
</HTML>
|
||||
121
doc/dump_h5md.txt
Normal file
121
doc/dump_h5md.txt
Normal file
@ -0,0 +1,121 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
dump h5md command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
dump ID group-ID h5md N file.h5 args :pre
|
||||
|
||||
ID = user-assigned name for the dump :ulb,l
|
||||
group-ID = ID of the group of atoms to be imaged :l
|
||||
h5md = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
|
||||
N = dump every this many timesteps :l
|
||||
file.h5 = name of file to write to :l
|
||||
args = list of data elements to dump, with their dump "subintervals".
|
||||
At least one element must be given and image may only be present if
|
||||
position is specified first. :l
|
||||
position options
|
||||
image
|
||||
velocity options
|
||||
force options
|
||||
species options
|
||||
file_from ID: do not open a new file, re-use the already opened file from dump ID
|
||||
box value = {yes} or {no}
|
||||
create_group value = {yes} or {no}
|
||||
author value = quoted string :pre
|
||||
|
||||
For the elements {position}, {velocity}, {force} and {species}, one may specify
|
||||
a sub-interval to write the data only every N_element iterations of the dump
|
||||
(i.e. every N*N_element time steps). This is specified by the option
|
||||
|
||||
every N_element :pre
|
||||
|
||||
that follows directly the element declaration.
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
dump h5md1 all h5md 100 dump_h5md.h5 position image
|
||||
dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10 :pre
|
||||
dump h5md1 all h5md 100 dump_h5md.h5 velocity author "L. Ammps" :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Dump a snapshot of atom coordinates every N timesteps in the "HDF5"_HDF5_ws
|
||||
based "H5MD"_h5md file format "(de Buyl et al.)"_#h5md_cpc.
|
||||
HDF5 files are binary, portable and self-describing.
|
||||
This dump style will write only one file, on the root node.
|
||||
|
||||
Several dumps may write to the same file, by using file_from and referring to a
|
||||
previously defined dump.
|
||||
Several groups may also be stored within the same file by defining several dumps.
|
||||
A dump that refers (via {file_from}) to an already open dump ID and that
|
||||
concerns another particle group must specify {create_group yes}.
|
||||
|
||||
:link(h5md,http://nongnu.org/h5md/)
|
||||
|
||||
Each data element is written every N*N_element steps. For {image}, no
|
||||
subinterval is needed as it must be present at the same interval as {position}.
|
||||
{image} must be given after {position} in any case.
|
||||
The box information (edges in each dimension) is stored at the same interval
|
||||
than the {position} element, if present. Else it is stored every N steps.
|
||||
|
||||
IMPORTANT NOTE: Because periodic boundary conditions are enforced only
|
||||
on timesteps when neighbor lists are rebuilt, the coordinates of an
|
||||
atom written to a dump file may be slightly outside the simulation
|
||||
box.
|
||||
|
||||
[Use from write_dump:]
|
||||
|
||||
It is possible to use this dump style with the "write_dump"_write_dump.html command.
|
||||
In this case, the subintervals must not be set at all.
|
||||
{write_dump} can be used either alone or in conjunction with {file_from} so that
|
||||
fixed-in-time data can be stored in the same file as time-dependent data.
|
||||
|
||||
Typically, the {species} data is fixed. The following two commands store the
|
||||
position data every 100 timesteps, with the image data, and store once the
|
||||
species data in the same file.
|
||||
|
||||
dump h5md1 all h5md 100 dump.h5 position image
|
||||
write_dump all h5md dump.h5 file_from h5md1 species :pre
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
:ulb
|
||||
The number of atoms per snapshot cannot change with the h5md style. :l
|
||||
The position data is stored wrapped (box boundaries not enforced, see note above). :l
|
||||
Only orthogonal domains are currently supported. This is a limitation of the
|
||||
present package and not of H5MD itself. :l
|
||||
:ule
|
||||
|
||||
The {h5md} dump style is part of the USER-H5MD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info. It also requires
|
||||
(i) building the ch5md library provided with LAMMPS (See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.) and
|
||||
(ii) having the "HDF5"_HDF5_ws library installed (C bindings are sufficient).
|
||||
The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library.
|
||||
|
||||
:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
|
||||
|
||||
:line
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
|
||||
|
||||
:line
|
||||
|
||||
:link(h5md_cpc)
|
||||
[(de Buyl et al.)] de Buyl, Colberg and Hofling, H5MD: A structured, efficient,
|
||||
and portable file format for molecular data, Comp. Phys. Comm. 185(6),
|
||||
1546-1553 (2014) - "\[arXiv:1308.6382\]"_http://arxiv.org/abs/1308.6382/.
|
||||
25
lib/ch5md/LICENSE
Normal file
25
lib/ch5md/LICENSE
Normal file
@ -0,0 +1,25 @@
|
||||
Copyright (C) 2013-2014 Pierre de Buyl
|
||||
|
||||
All rights reserved.
|
||||
|
||||
Redistribution and use in source and binary forms, with or without
|
||||
modification, are permitted provided that the following conditions are met:
|
||||
a. Redistributions of source code must retain the above copyright
|
||||
notice, this list of conditions and the following disclaimer.
|
||||
b. Redistributions in binary form must reproduce the above copyright
|
||||
notice, this list of conditions and the following disclaimer in the
|
||||
documentation and/or other materials provided with the distribution.
|
||||
c. Neither the name of the <organization> nor the
|
||||
names of its contributors may be used to endorse or promote products
|
||||
derived from this software without specific prior written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
|
||||
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
|
||||
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
|
||||
DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE FOR ANY
|
||||
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
|
||||
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
|
||||
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
|
||||
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
|
||||
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
||||
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
32
lib/ch5md/Makefile
Normal file
32
lib/ch5md/Makefile
Normal file
@ -0,0 +1,32 @@
|
||||
EXTRAMAKE=Makefile.lammps.empty
|
||||
|
||||
CC=h5cc
|
||||
HDF5_PATH=/usr
|
||||
INC=-I include
|
||||
AR=ar
|
||||
ARFLAGS=rc
|
||||
LIB=libch5md.a
|
||||
|
||||
all: lib Makefile.lammps
|
||||
|
||||
build:
|
||||
mkdir -p build
|
||||
build/ch5md.o: src/ch5md.c | build
|
||||
$(CC) $(INC) -c $< -o $@
|
||||
|
||||
.PHONY: Makefile.lammps
|
||||
Makefile.lammps:
|
||||
@echo "# Settings that the LAMMPS build will import when this package library is used" > Makefile.lammps
|
||||
ifneq "$(HDF5_PATH)" "/usr"
|
||||
@echo "ch5md_SYSINC = -I${HDF5_PATH}/include" >> Makefile.lammps
|
||||
@echo "ch5md_SYSLIB = -L${HDF5_PATH}/lib" >> Makefile.lammps
|
||||
endif
|
||||
|
||||
$(LIB): build/ch5md.o
|
||||
$(AR) $(ARFLAGS) $(LIB) build/ch5md.o
|
||||
|
||||
lib: $(LIB) Makefile.lammps
|
||||
|
||||
clean:
|
||||
rm -f build/*.o $(LIB) Makefile.lammps
|
||||
|
||||
20
lib/ch5md/README
Normal file
20
lib/ch5md/README
Normal file
@ -0,0 +1,20 @@
|
||||
ch5md : Read and write H5MD files in C
|
||||
======================================
|
||||
|
||||
Copyright (C) 2013-2014 Pierre de Buyl
|
||||
|
||||
ch5md is a set of C routines to manipulate H5MD files. H5MD is a file format
|
||||
specification based on [HDF5](http://www.hdfgroup.org/HDF5/) for storing
|
||||
molecular data, whose development is found at <http://nongnu.org/h5md/>.
|
||||
|
||||
ch5md is developped by Pierre de Buyl and is released under the 3-clause BSD
|
||||
license that can be found in the file LICENSE.
|
||||
|
||||
To use the h5md dump style in lammps, execute make in this directory then 'make
|
||||
yes-user-h5md' in the src directory of lammps. Rebuild lammps.
|
||||
|
||||
If HDF5 is not in a standard system location, use `make HDF5_PATH=/path/to/hdf5`.
|
||||
|
||||
In the case of 2015 and more recent debian and ubuntu systems where concurrent
|
||||
serial and mpi are possible, use the full platform depedent path, i.e.
|
||||
`HDF5_PATH=/usr/lib/x86_64-linux-gnu/hdf5/serial`
|
||||
73
lib/ch5md/include/ch5md.h
Normal file
73
lib/ch5md/include/ch5md.h
Normal file
@ -0,0 +1,73 @@
|
||||
/* This file is part of ch5md
|
||||
* Copyright (C) 2013-2015 Pierre de Buyl
|
||||
* All rights reserved.
|
||||
*
|
||||
* This software may be modified and distributed under the terms
|
||||
* of the BSD license. See the LICENSE file for details.
|
||||
*/
|
||||
|
||||
#ifndef CH5MD_H
|
||||
#define CH5MD_H
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
#include "hdf5.h"
|
||||
#include <stdbool.h>
|
||||
|
||||
#define CH5MD_RANK_ERROR -10
|
||||
|
||||
typedef struct h5md_element_struct {
|
||||
hid_t group;
|
||||
hid_t step;
|
||||
hid_t time;
|
||||
hid_t value;
|
||||
hid_t datatype;
|
||||
int is_time;
|
||||
int current_step;
|
||||
struct h5md_element_struct *link;
|
||||
struct h5md_particles_group_struct *particles_group;
|
||||
} h5md_element;
|
||||
|
||||
typedef struct h5md_particles_group_struct {
|
||||
hid_t group;
|
||||
h5md_element position;
|
||||
hid_t box;
|
||||
h5md_element box_edges;
|
||||
h5md_element image;
|
||||
h5md_element velocity;
|
||||
h5md_element force;
|
||||
h5md_element mass;
|
||||
h5md_element species;
|
||||
h5md_element id;
|
||||
h5md_element charge;
|
||||
int local_size_max;
|
||||
} h5md_particles_group;
|
||||
|
||||
typedef struct {
|
||||
hid_t id;
|
||||
int version[2];
|
||||
hid_t particles;
|
||||
hid_t observables;
|
||||
hid_t parameters;
|
||||
} h5md_file;
|
||||
|
||||
h5md_file h5md_create_file (const char *filename, const char *author, const char *author_email, const char *creator, const char *creator_version);
|
||||
int h5md_close_file(h5md_file file);
|
||||
hid_t h5md_open_file (const char *filename);
|
||||
h5md_particles_group h5md_create_particles_group(h5md_file file, const char *name);
|
||||
h5md_element h5md_create_time_data(hid_t loc, const char *name, int rank, int int_dims[], hid_t datatype, h5md_element *link);
|
||||
int h5md_close_element(h5md_element e);
|
||||
h5md_element h5md_create_fixed_data_simple(hid_t loc, const char *name, int rank, int int_dims[], hid_t datatype, void *data);
|
||||
h5md_element h5md_create_fixed_data_scalar(hid_t loc, const char *name, hid_t datatype, void *data);
|
||||
int h5md_append(h5md_element e, void *data, int step, double time);
|
||||
int h5md_create_box(h5md_particles_group *group, int dim, char *boundary[], bool is_time, double value[], h5md_element *link);
|
||||
int h5md_write_string_attribute(hid_t loc, const char *obj_name,
|
||||
const char *att_name, const char *value);
|
||||
|
||||
#ifdef __cplusplus
|
||||
}
|
||||
#endif
|
||||
|
||||
#endif
|
||||
444
lib/ch5md/src/ch5md.c
Normal file
444
lib/ch5md/src/ch5md.c
Normal file
@ -0,0 +1,444 @@
|
||||
/* This file is part of ch5md
|
||||
* Copyright (C) 2013-2015 Pierre de Buyl
|
||||
* All rights reserved.
|
||||
*
|
||||
* This software may be modified and distributed under the terms
|
||||
* of the BSD license. See the LICENSE file for details.
|
||||
*/
|
||||
|
||||
#include "hdf5.h"
|
||||
#include "ch5md.h"
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
#define MIN_CHUNK 10
|
||||
#define MAX_CHUNK 256
|
||||
#define MAX_RANK 5
|
||||
|
||||
h5md_file h5md_create_file (const char *filename, const char *author, const char *author_email, const char *creator, const char *creator_version)
|
||||
{
|
||||
h5md_file file;
|
||||
hid_t g, g1;
|
||||
hid_t a, s, t;
|
||||
hsize_t dims[1];
|
||||
herr_t status;
|
||||
|
||||
file.version[0] = 1;
|
||||
file.version[1] = 0;
|
||||
|
||||
file.id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
|
||||
g = H5Gcreate(file.id, "h5md", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
|
||||
dims[0] = 2;
|
||||
s = H5Screate_simple(1, dims, NULL);
|
||||
a = H5Acreate(g, "version", H5T_NATIVE_INT, s, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Awrite(a, H5T_NATIVE_INT, file.version);
|
||||
status = H5Aclose(a);
|
||||
status = H5Sclose(s);
|
||||
|
||||
s = H5Screate(H5S_SCALAR);
|
||||
|
||||
g1 = H5Gcreate(g, "author", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
t = H5Tcopy(H5T_C_S1);
|
||||
status = H5Tset_size(t, strlen(author));
|
||||
a = H5Acreate(g1, "name", t, s, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Awrite(a, t, author);
|
||||
status = H5Aclose(a);
|
||||
status = H5Tclose(t);
|
||||
if (NULL!=author_email) {
|
||||
t = H5Tcopy(H5T_C_S1);
|
||||
status = H5Tset_size(t, strlen(author_email));
|
||||
a = H5Acreate(g1, "author_email", t, s, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Awrite(a, t, author_email);
|
||||
status = H5Aclose(a);
|
||||
status = H5Tclose(t);
|
||||
}
|
||||
status = H5Gclose(g1);
|
||||
|
||||
g1 = H5Gcreate(g, "creator", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
t = H5Tcopy(H5T_C_S1);
|
||||
status = H5Tset_size(t, strlen(creator));
|
||||
a = H5Acreate(g1, "name", t, s, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Awrite(a, t, creator);
|
||||
status = H5Aclose(a);
|
||||
status = H5Tclose(t);
|
||||
t = H5Tcopy(H5T_C_S1);
|
||||
status = H5Tset_size(t, strlen(creator_version));
|
||||
a = H5Acreate(g1, "version", t, s, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Awrite(a, t, creator_version);
|
||||
status = H5Aclose(a);
|
||||
status = H5Tclose(t);
|
||||
status = H5Gclose(g1);
|
||||
|
||||
file.particles = H5Gcreate(file.id, "particles", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
file.observables = H5Gcreate(file.id, "observables", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
file.parameters = H5Gcreate(file.id, "parameters", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
|
||||
return file;
|
||||
}
|
||||
|
||||
int h5md_close_file(h5md_file file) {
|
||||
H5Gclose(file.particles);
|
||||
H5Gclose(file.observables);
|
||||
H5Gclose(file.parameters);
|
||||
H5Fclose(file.id);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
hid_t h5md_open_file (const char *filename)
|
||||
{
|
||||
hid_t file;
|
||||
hid_t g;
|
||||
hid_t a, s;
|
||||
hsize_t dims[1];
|
||||
int version[2];
|
||||
int version_ok;
|
||||
|
||||
file = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
|
||||
|
||||
g = H5Gopen(file, "h5md", H5P_DEFAULT);
|
||||
|
||||
version_ok = false;
|
||||
dims[0] = 2;
|
||||
a = H5Aopen(g, "version", H5P_DEFAULT);
|
||||
s = H5Aget_space(a);
|
||||
if (!(H5Sis_simple(s)>0)) {
|
||||
printf("H5MD version is not a simple dataspace");
|
||||
H5Sclose(s);
|
||||
H5Aclose(a);
|
||||
H5Gclose(g);
|
||||
H5Fclose(file);
|
||||
} else {
|
||||
if (H5Sget_simple_extent_ndims(s)==1) {
|
||||
H5Sget_simple_extent_dims(s, dims, NULL);
|
||||
if (dims[0]==2) {
|
||||
H5Aread(a, H5T_NATIVE_INT, version);
|
||||
if ( (version[0]==1) && (version[1]==0) ) {version_ok = true;}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
H5Aclose(a);
|
||||
H5Sclose(s);
|
||||
H5Gclose(g);
|
||||
|
||||
if (!version_ok) H5Fclose(file);
|
||||
|
||||
return file;
|
||||
|
||||
}
|
||||
|
||||
h5md_particles_group h5md_create_particles_group(h5md_file file, const char *name)
|
||||
{
|
||||
h5md_particles_group group;
|
||||
|
||||
group.group = H5Gcreate(file.particles, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
|
||||
return group;
|
||||
}
|
||||
|
||||
h5md_element h5md_create_time_data(hid_t loc, const char *name, int rank, int int_dims[], hid_t datatype, h5md_element *link)
|
||||
{
|
||||
|
||||
h5md_element td;
|
||||
|
||||
hid_t spc, plist;
|
||||
hsize_t dims[MAX_RANK], max_dims[MAX_RANK], chunks[MAX_RANK];
|
||||
herr_t status;
|
||||
|
||||
int i;
|
||||
|
||||
dims[0] = 0 ;
|
||||
max_dims[0] = H5S_UNLIMITED ;
|
||||
for (i=0; i<rank; i++) {
|
||||
dims[i+1] = int_dims[i];
|
||||
max_dims[i+1] = int_dims[i];
|
||||
}
|
||||
chunks[0] = 1 ;
|
||||
if (MAX_CHUNK<int_dims[0]/4) {
|
||||
chunks[1] = MAX_CHUNK;
|
||||
} else {
|
||||
chunks[1] = int_dims[0];
|
||||
}
|
||||
for (i=1; i<rank; i++) {
|
||||
chunks[i+1]=int_dims[i];
|
||||
}
|
||||
|
||||
td.group = H5Gcreate(loc, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
|
||||
if (NULL==link) {
|
||||
spc = H5Screate_simple( 1 , dims, max_dims);
|
||||
plist = H5Pcreate(H5P_DATASET_CREATE);
|
||||
status = H5Pset_chunk(plist, 1, chunks);
|
||||
td.time = H5Dcreate(td.group, "time", H5T_NATIVE_DOUBLE, spc, H5P_DEFAULT, plist, H5P_DEFAULT);
|
||||
td.step = H5Dcreate(td.group, "step", H5T_NATIVE_INT, spc, H5P_DEFAULT, plist, H5P_DEFAULT);
|
||||
H5Pclose(plist);
|
||||
H5Sclose(spc);
|
||||
td.link=NULL;
|
||||
} else {
|
||||
td.link = link;
|
||||
status = H5Lcreate_hard(link->group, "step", td.group, "step", H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Lcreate_hard(link->group, "time", td.group, "time", H5P_DEFAULT, H5P_DEFAULT);
|
||||
}
|
||||
|
||||
spc = H5Screate_simple( rank+1 , dims, max_dims) ;
|
||||
plist = H5Pcreate(H5P_DATASET_CREATE);
|
||||
status = H5Pset_chunk(plist, rank+1, chunks);
|
||||
td.value = H5Dcreate(td.group, "value", datatype, spc, H5P_DEFAULT, plist, H5P_DEFAULT);
|
||||
H5Pclose(plist);
|
||||
status = H5Sclose(spc);
|
||||
|
||||
td.datatype = datatype;
|
||||
td.is_time = true;
|
||||
|
||||
return td;
|
||||
|
||||
}
|
||||
|
||||
int h5md_close_element(h5md_element e)
|
||||
{
|
||||
herr_t status;
|
||||
|
||||
if (!e.is_time) return 0;
|
||||
|
||||
if (e.link==NULL) {
|
||||
status = H5Dclose(e.step);
|
||||
status = H5Dclose(e.time);
|
||||
}
|
||||
status = H5Dclose(e.value);
|
||||
status = H5Gclose(e.group);
|
||||
|
||||
return 0;
|
||||
|
||||
}
|
||||
|
||||
h5md_element h5md_create_fixed_data_simple(hid_t loc, const char *name, int rank, int int_dims[], hid_t datatype, void *data)
|
||||
{
|
||||
|
||||
h5md_element fd;
|
||||
|
||||
hid_t spc;
|
||||
hsize_t dims[H5S_MAX_RANK];
|
||||
herr_t status;
|
||||
int i;
|
||||
|
||||
for (i=0; i<rank; i++) {
|
||||
dims[i] = int_dims[i];
|
||||
}
|
||||
|
||||
spc = H5Screate_simple(rank, dims, NULL);
|
||||
fd.value = H5Dcreate(loc, name, datatype, spc, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Sclose(spc);
|
||||
status = H5Dwrite(fd.value, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
|
||||
status = H5Dclose(fd.value);
|
||||
|
||||
fd.is_time = false;
|
||||
|
||||
return fd;
|
||||
|
||||
}
|
||||
|
||||
h5md_element h5md_create_fixed_data_scalar(hid_t loc, const char *name, hid_t datatype, void *data)
|
||||
{
|
||||
|
||||
h5md_element fd;
|
||||
|
||||
hid_t spc;
|
||||
herr_t status;
|
||||
|
||||
spc = H5Screate(H5S_SCALAR);
|
||||
fd.value = H5Dcreate(loc, name, datatype, spc, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Sclose(spc);
|
||||
status = H5Dwrite(fd.value, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
|
||||
status = H5Dclose(fd.value);
|
||||
|
||||
fd.is_time = false;
|
||||
|
||||
return fd;
|
||||
|
||||
}
|
||||
|
||||
int h5md_extend_by_one(hid_t dset, hsize_t *dims) {
|
||||
|
||||
hid_t file_space;
|
||||
int rank;
|
||||
hsize_t maxdims[H5S_MAX_RANK];
|
||||
|
||||
// Get dataset information
|
||||
file_space = H5Dget_space(dset);
|
||||
rank = H5Sget_simple_extent_ndims(file_space);
|
||||
if (rank > H5S_MAX_RANK) {
|
||||
return CH5MD_RANK_ERROR;
|
||||
}
|
||||
H5Sget_simple_extent_dims(file_space, dims, maxdims);
|
||||
H5Sclose(file_space);
|
||||
|
||||
// Extend dimensions by one
|
||||
dims[0] = dims[0]+1;
|
||||
H5Dset_extent(dset, dims);
|
||||
|
||||
return 0;
|
||||
|
||||
}
|
||||
|
||||
int h5md_append(h5md_element e, void *data, int step, double time) {
|
||||
|
||||
hid_t mem_space, file_space;
|
||||
int i, rank;
|
||||
hsize_t dims[H5S_MAX_RANK];
|
||||
hsize_t start[H5S_MAX_RANK], count[H5S_MAX_RANK];
|
||||
|
||||
// If not a time-dependent H5MD element, do nothing
|
||||
if (!e.is_time) return 0;
|
||||
|
||||
if (NULL==e.link) {
|
||||
h5md_extend_by_one(e.step, dims);
|
||||
|
||||
// Define hyperslab selection
|
||||
start[0] = dims[0]-1;
|
||||
count[0] = 1;
|
||||
|
||||
// Select the hyperslab
|
||||
file_space = H5Dget_space(e.step);
|
||||
rank = H5Sget_simple_extent_ndims(file_space);
|
||||
mem_space = H5Screate_simple(rank-1, dims+1, NULL);
|
||||
// Define hyperslab selection
|
||||
start[0] = dims[0]-1;
|
||||
count[0] = 1;
|
||||
for (i=1 ; i<rank ; i++) {
|
||||
start[i] = 0;
|
||||
count[i] = dims[i];
|
||||
}
|
||||
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
|
||||
H5Dwrite(e.step, H5T_NATIVE_INT, mem_space, file_space, H5P_DEFAULT, (void *)&step);
|
||||
H5Sclose(file_space);
|
||||
H5Sclose(mem_space);
|
||||
|
||||
h5md_extend_by_one(e.time, dims);
|
||||
|
||||
// Define hyperslab selection
|
||||
start[0] = dims[0]-1;
|
||||
count[0] = 1;
|
||||
|
||||
// Select the hyperslab
|
||||
file_space = H5Dget_space(e.time);
|
||||
rank = H5Sget_simple_extent_ndims(file_space);
|
||||
mem_space = H5Screate_simple(rank-1, dims+1, NULL);
|
||||
// Define hyperslab selection
|
||||
start[0] = dims[0]-1;
|
||||
count[0] = 1;
|
||||
for (i=1 ; i<rank ; i++) {
|
||||
start[i] = 0;
|
||||
count[i] = dims[i];
|
||||
}
|
||||
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
|
||||
H5Dwrite(e.time, H5T_NATIVE_DOUBLE, mem_space, file_space, H5P_DEFAULT, (void *)&time);
|
||||
H5Sclose(file_space);
|
||||
H5Sclose(mem_space);
|
||||
}
|
||||
|
||||
h5md_extend_by_one(e.value, dims);
|
||||
|
||||
// Select the hyperslab
|
||||
file_space = H5Dget_space(e.value);
|
||||
rank = H5Sget_simple_extent_ndims(file_space);
|
||||
mem_space = H5Screate_simple(rank-1, dims+1, NULL);
|
||||
|
||||
// Define hyperslab selection
|
||||
start[0] = dims[0]-1;
|
||||
count[0] = 1;
|
||||
for (i=1 ; i<rank ; i++) {
|
||||
start[i] = 0;
|
||||
count[i] = dims[i];
|
||||
}
|
||||
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
|
||||
H5Dwrite(e.value, e.datatype, mem_space, file_space, H5P_DEFAULT, data);
|
||||
H5Sclose(file_space);
|
||||
H5Sclose(mem_space);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
int h5md_create_box(h5md_particles_group *group, int dim, char *boundary[], bool is_time, double value[], h5md_element *link)
|
||||
{
|
||||
hid_t spc, att, t;
|
||||
hsize_t dims[1];
|
||||
int int_dims[1];
|
||||
herr_t status;
|
||||
int i;
|
||||
size_t boundary_length, tmp;
|
||||
//char *tmp_boundary;
|
||||
|
||||
// Create box group
|
||||
group->box = H5Gcreate(group->group, "box", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
|
||||
// Create dimension attribute
|
||||
spc = H5Screate(H5S_SCALAR);
|
||||
att = H5Acreate(group->box, "dimension", H5T_NATIVE_INT, spc, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Awrite(att, H5T_NATIVE_INT, &dim);
|
||||
status = H5Aclose(att);
|
||||
status = H5Sclose(spc);
|
||||
|
||||
// Compute the size of the string type for boundary
|
||||
dims[0] = dim;
|
||||
boundary_length=0;
|
||||
for (i=0; i<dim; i++) {
|
||||
tmp = strlen(boundary[i])+1;
|
||||
if (tmp>boundary_length) {
|
||||
boundary_length=tmp;
|
||||
}
|
||||
}
|
||||
char *tmp_boundary = malloc(dim*sizeof(char)*boundary_length);
|
||||
for (i=0; i<dim; i++) {
|
||||
strcpy((tmp_boundary+i*boundary_length), boundary[i]);
|
||||
}
|
||||
// Create boundary attribute
|
||||
t = H5Tcopy(H5T_C_S1);
|
||||
status = H5Tset_size(t, boundary_length);
|
||||
spc = H5Screate_simple(1, dims, NULL);
|
||||
att = H5Acreate(group->box, "boundary", t, spc, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Awrite(att, t, tmp_boundary);
|
||||
free(tmp_boundary);
|
||||
status = H5Aclose(att);
|
||||
status = H5Sclose(spc);
|
||||
status = H5Tclose(t);
|
||||
|
||||
// Create edges
|
||||
// Check if the box is time-dependent or not
|
||||
int_dims[0]=dim;
|
||||
if (is_time) {
|
||||
group->box_edges = h5md_create_time_data(group->box, "edges", 1, int_dims, H5T_NATIVE_DOUBLE, link);
|
||||
} else {
|
||||
if (NULL!=value) {
|
||||
group->box_edges = h5md_create_fixed_data_simple(group->box, "edges", 1, int_dims, H5T_NATIVE_DOUBLE, value);
|
||||
}
|
||||
}
|
||||
|
||||
status = H5Gclose(group->box);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
int h5md_write_string_attribute(hid_t loc, const char *obj_name,
|
||||
const char *att_name, const char *value)
|
||||
{
|
||||
hid_t obj;
|
||||
hid_t s, t, a;
|
||||
herr_t status;
|
||||
|
||||
obj = H5Oopen(loc, obj_name, H5P_DEFAULT);
|
||||
|
||||
t = H5Tcopy(H5T_C_S1);
|
||||
status = H5Tset_size(t, strlen(value));
|
||||
s = H5Screate(H5S_SCALAR);
|
||||
a = H5Acreate(obj, att_name, t, s, H5P_DEFAULT, H5P_DEFAULT);
|
||||
status = H5Awrite(a, t, value);
|
||||
status = H5Aclose(a);
|
||||
status = H5Sclose(s);
|
||||
status = H5Tclose(t);
|
||||
|
||||
status = H5Oclose(obj);
|
||||
|
||||
return 0;
|
||||
}
|
||||
64
src/USER-H5MD/Install.sh
Normal file
64
src/USER-H5MD/Install.sh
Normal file
@ -0,0 +1,64 @@
|
||||
# Install/unInstall package files in LAMMPS
|
||||
# mode = 0/1/2 for uninstall/install/update
|
||||
|
||||
mode=$1
|
||||
|
||||
# arg1 = file, arg2 = file it depends on
|
||||
|
||||
action () {
|
||||
if (test $mode = 0) then
|
||||
rm -f ../$1
|
||||
elif (! cmp -s $1 ../$1) then
|
||||
if (test -z "$2" || test -e ../$2) then
|
||||
cp $1 ..
|
||||
if (test $mode = 2) then
|
||||
echo " updating src/$1"
|
||||
fi
|
||||
fi
|
||||
elif (test -n "$2") then
|
||||
if (test ! -e ../$2) then
|
||||
rm -f ../$1
|
||||
fi
|
||||
fi
|
||||
}
|
||||
|
||||
for file in *.cpp *.h; do
|
||||
action $file
|
||||
done
|
||||
|
||||
# edit 2 Makefile.package files to include/exclude package info
|
||||
|
||||
if (test $1 = 1) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's/[^ \t]*ch5md[^ \t]* //g' ../Makefile.package
|
||||
sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/ch5md\/include |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/ch5md |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_LIB =[ \t]*|&-lch5md |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_LIB =[ \t]*|&-lhdf5 |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(ch5md_SYSINC) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(ch5md_SYSLIB) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(ch5md_SYSPATH) |' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
sed -i -e '/^include.*ch5md.*$/d' ../Makefile.package.settings
|
||||
# multiline form needed for BSD sed on Macs
|
||||
sed -i -e '4 i \
|
||||
include ..\/..\/lib\/ch5md\/Makefile.lammps
|
||||
' ../Makefile.package.settings
|
||||
|
||||
fi
|
||||
|
||||
elif (test $1 = 0) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's/[^ \t]*ch5md[^ \t]* //g' ../Makefile.package
|
||||
sed -i -e 's/[^ \t]*hdf5[^ \t]* //g' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
sed -i -e '/^include.*ch5md.*$/d' ../Makefile.package.settings
|
||||
fi
|
||||
|
||||
fi
|
||||
8
src/USER-H5MD/README
Normal file
8
src/USER-H5MD/README
Normal file
@ -0,0 +1,8 @@
|
||||
This package provides the h5md dump style.
|
||||
|
||||
See the doc page for dump_h5md. This dump style requires building the bundled
|
||||
ch5md library and HDF5 (see lib/ch5md/README).
|
||||
|
||||
The person who created this package is Pierre de Buyl (KU Leuven), see
|
||||
http://pdebuyl.be/ for contact information. Contact him directly if you have
|
||||
questions.
|
||||
557
src/USER-H5MD/dump_h5md.cpp
Normal file
557
src/USER-H5MD/dump_h5md.cpp
Normal file
@ -0,0 +1,557 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
Contributing author: Pierre de Buyl (KU Leuven)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "limits.h"
|
||||
#include "ch5md.h"
|
||||
#include "dump_h5md.h"
|
||||
#include "domain.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "group.h"
|
||||
#include "output.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "version.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MYMIN(a,b) ((a) < (b) ? (a) : (b))
|
||||
#define MYMAX(a,b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
/** Scan common options for the dump elements
|
||||
*/
|
||||
int element_args(int narg, char **arg, int *every)
|
||||
{
|
||||
int iarg=0;
|
||||
while (iarg<narg) {
|
||||
if (strcmp(arg[iarg], "every")==0) {
|
||||
if (narg<2) return -1;
|
||||
*every = atoi(arg[iarg+1]);
|
||||
iarg+=2;
|
||||
} else {
|
||||
break;
|
||||
}
|
||||
}
|
||||
return iarg;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
|
||||
{
|
||||
if (narg<6) error->all(FLERR,"Illegal dump h5md command");
|
||||
if (binary || compressed || multifile || multiproc)
|
||||
error->all(FLERR,"Invalid dump h5md filename");
|
||||
|
||||
if (domain->triclinic!=0)
|
||||
error->all(FLERR,"Invalid domain for dump h5md. Only triclinic domains supported.");
|
||||
|
||||
size_one = 6;
|
||||
sort_flag = 1;
|
||||
sortcol = 0;
|
||||
format_default = NULL;
|
||||
flush_flag = 0;
|
||||
unwrap_flag = 0;
|
||||
datafile_from_dump = -1;
|
||||
author_name=NULL;
|
||||
|
||||
every_dump = force->inumeric(FLERR,arg[3]);
|
||||
every_position = every_image = -1;
|
||||
every_velocity = every_force = every_species = -1;
|
||||
every_charge = -1;
|
||||
|
||||
do_box=true;
|
||||
create_group=true;
|
||||
|
||||
bool box_is_set, create_group_is_set;
|
||||
box_is_set = create_group_is_set = false;
|
||||
int iarg=5;
|
||||
int n_parsed, default_every;
|
||||
size_one=0;
|
||||
if (every_dump==0) default_every=0; else default_every=1;
|
||||
|
||||
while (iarg<narg) {
|
||||
if (strcmp(arg[iarg], "position")==0) {
|
||||
every_position=default_every;
|
||||
iarg+=1;
|
||||
n_parsed = element_args(narg-iarg, &arg[iarg], &every_position);
|
||||
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
|
||||
iarg += n_parsed;
|
||||
size_one+=domain->dimension;
|
||||
} else if (strcmp(arg[iarg], "image")==0) {
|
||||
if (every_position<0) error->all(FLERR, "Illegal dump h5md command");
|
||||
iarg+=1;
|
||||
size_one+=domain->dimension;
|
||||
every_image = every_position;
|
||||
} else if (strcmp(arg[iarg], "velocity")==0) {
|
||||
every_velocity = default_every;
|
||||
iarg+=1;
|
||||
n_parsed = element_args(narg-iarg, &arg[iarg], &every_velocity);
|
||||
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
|
||||
iarg += n_parsed;
|
||||
size_one+=domain->dimension;
|
||||
} else if (strcmp(arg[iarg], "force")==0) {
|
||||
every_force = default_every;
|
||||
iarg+=1;
|
||||
n_parsed = element_args(narg-iarg, &arg[iarg], &every_force);
|
||||
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
|
||||
iarg += n_parsed;
|
||||
size_one+=domain->dimension;
|
||||
} else if (strcmp(arg[iarg], "species")==0) {
|
||||
every_species=default_every;
|
||||
iarg+=1;
|
||||
n_parsed = element_args(narg-iarg, &arg[iarg], &every_species);
|
||||
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
|
||||
iarg += n_parsed;
|
||||
size_one+=1;
|
||||
} else if (strcmp(arg[iarg], "charge")==0) {
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR, "Requesting non-allocated quantity q in dump_h5md");
|
||||
every_charge = default_every;
|
||||
iarg+=1;
|
||||
n_parsed = element_args(narg-iarg, &arg[iarg], &every_charge);
|
||||
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
|
||||
iarg += n_parsed;
|
||||
size_one+=1;
|
||||
} else if (strcmp(arg[iarg], "file_from")==0) {
|
||||
if (iarg+1>=narg) {
|
||||
error->all(FLERR, "Invalid number of arguments in dump h5md");
|
||||
}
|
||||
if (box_is_set||create_group_is_set)
|
||||
error->all(FLERR, "Cannot set file_from in dump h5md after box or create_group");
|
||||
int idump;
|
||||
for (idump = 0; idump < output->ndump; idump++)
|
||||
if (strcmp(arg[iarg+1],output->dump[idump]->id) == 0) break;
|
||||
if (idump == output->ndump) error->all(FLERR,"Cound not find dump_modify ID");
|
||||
datafile_from_dump = idump;
|
||||
do_box=false;
|
||||
create_group=false;
|
||||
iarg+=2;
|
||||
} else if (strcmp(arg[iarg], "box")==0) {
|
||||
if (iarg+1>=narg) {
|
||||
error->all(FLERR, "Invalid number of arguments in dump h5md");
|
||||
}
|
||||
box_is_set = true;
|
||||
if (strcmp(arg[iarg+1], "yes")==0)
|
||||
do_box=true;
|
||||
else if (strcmp(arg[iarg+1], "no")==0)
|
||||
do_box=false;
|
||||
else
|
||||
error->all(FLERR, "Illegal dump h5md command");
|
||||
iarg+=2;
|
||||
} else if (strcmp(arg[iarg], "create_group")==0) {
|
||||
if (iarg+1>=narg) {
|
||||
error->all(FLERR, "Invalid number of arguments in dump h5md");
|
||||
}
|
||||
create_group_is_set = true;
|
||||
if (strcmp(arg[iarg+1], "yes")==0)
|
||||
create_group=true;
|
||||
else if (strcmp(arg[iarg+1], "no")==0) {
|
||||
create_group=false;
|
||||
}
|
||||
else
|
||||
error->all(FLERR, "Illegal dump h5md command");
|
||||
iarg+=2;
|
||||
} else if (strcmp(arg[iarg], "author")==0) {
|
||||
if (iarg+1>=narg) {
|
||||
error->all(FLERR, "Invalid number of arguments in dump h5md");
|
||||
}
|
||||
if (author_name==NULL) {
|
||||
author_name = new char[strlen(arg[iarg]+1)];
|
||||
strcpy(author_name, arg[iarg+1]);
|
||||
} else {
|
||||
error->all(FLERR, "Illegal dump h5md command: author argument repeated");
|
||||
}
|
||||
iarg+=2;
|
||||
} else {
|
||||
error->all(FLERR, "Invalid argument to dump h5md");
|
||||
}
|
||||
}
|
||||
|
||||
// allocate global array for atom coords
|
||||
|
||||
bigint n = group->count(igroup);
|
||||
natoms = static_cast<int> (n);
|
||||
|
||||
if (every_position>=0)
|
||||
memory->create(dump_position,domain->dimension*natoms,"dump:position");
|
||||
if (every_image>=0)
|
||||
memory->create(dump_image,domain->dimension*natoms,"dump:image");
|
||||
if (every_velocity>=0)
|
||||
memory->create(dump_velocity,domain->dimension*natoms,"dump:velocity");
|
||||
if (every_force>=0)
|
||||
memory->create(dump_force,domain->dimension*natoms,"dump:force");
|
||||
if (every_species>=0)
|
||||
memory->create(dump_species,natoms,"dump:species");
|
||||
if (every_charge>=0)
|
||||
memory->create(dump_charge,natoms,"dump:charge");
|
||||
|
||||
openfile();
|
||||
ntotal = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DumpH5MD::~DumpH5MD()
|
||||
{
|
||||
if (every_position>=0) {
|
||||
memory->destroy(dump_position);
|
||||
if (me==0) {
|
||||
h5md_close_element(particles_data.position);
|
||||
if (do_box)
|
||||
h5md_close_element(particles_data.box_edges);
|
||||
}
|
||||
}
|
||||
if (every_image>=0) {
|
||||
memory->destroy(dump_image);
|
||||
if (me==0) h5md_close_element(particles_data.image);
|
||||
}
|
||||
if (every_velocity>=0) {
|
||||
memory->destroy(dump_velocity);
|
||||
if (me==0) h5md_close_element(particles_data.velocity);
|
||||
}
|
||||
if (every_force>=0) {
|
||||
memory->destroy(dump_force);
|
||||
if (me==0) h5md_close_element(particles_data.force);
|
||||
}
|
||||
if (every_species>=0) {
|
||||
memory->destroy(dump_species);
|
||||
if (me==0) h5md_close_element(particles_data.species);
|
||||
}
|
||||
if (every_charge>=0) {
|
||||
memory->destroy(dump_charge);
|
||||
if (me==0) h5md_close_element(particles_data.charge);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::init_style()
|
||||
{
|
||||
if (sort_flag == 0 || sortcol != 0)
|
||||
error->all(FLERR,"Dump h5md requires sorting by atom ID");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::openfile()
|
||||
{
|
||||
char *group_name;
|
||||
int group_name_length;
|
||||
int dims[2];
|
||||
char *boundary[3];
|
||||
for (int i=0; i<3; i++) {
|
||||
boundary[i] = new char[9];
|
||||
if (domain->periodicity[i]==1) {
|
||||
strcpy(boundary[i], "periodic");
|
||||
} else {
|
||||
strcpy(boundary[i], "none");
|
||||
}
|
||||
}
|
||||
|
||||
if (me == 0) {
|
||||
if (datafile_from_dump<0) {
|
||||
if (author_name==NULL) {
|
||||
datafile = h5md_create_file(filename, "N/A", NULL, "lammps", LAMMPS_VERSION);
|
||||
} else {
|
||||
datafile = h5md_create_file(filename, author_name, NULL, "lammps", LAMMPS_VERSION);
|
||||
}
|
||||
group_name_length = strlen(group->names[igroup]);
|
||||
group_name = new char[group_name_length];
|
||||
strcpy(group_name, group->names[igroup]);
|
||||
if (create_group) {
|
||||
particles_data = h5md_create_particles_group(datafile, group_name);
|
||||
} else {
|
||||
particles_data.group = H5Gopen(datafile.particles, group_name, H5P_DEFAULT);
|
||||
}
|
||||
delete [] group_name;
|
||||
dims[0] = natoms;
|
||||
dims[1] = domain->dimension;
|
||||
if (every_position>0) {
|
||||
particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
|
||||
}
|
||||
if (every_image>0)
|
||||
particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
|
||||
if (every_velocity>0)
|
||||
particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
if (every_force>0)
|
||||
particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
if (every_species>0)
|
||||
particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
|
||||
if (every_charge>0) {
|
||||
particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
|
||||
}
|
||||
} else {
|
||||
DumpH5MD* other_dump;
|
||||
other_dump=(DumpH5MD*)output->dump[datafile_from_dump];
|
||||
datafile = other_dump->datafile;
|
||||
group_name_length = strlen(group->names[igroup]);
|
||||
group_name = new char[group_name_length];
|
||||
strcpy(group_name, group->names[igroup]);
|
||||
if (create_group) {
|
||||
particles_data = h5md_create_particles_group(datafile, group_name);
|
||||
} else {
|
||||
particles_data = other_dump->particles_data;
|
||||
}
|
||||
dims[0] = natoms;
|
||||
dims[1] = domain->dimension;
|
||||
if (every_position>0) {
|
||||
particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
|
||||
}
|
||||
if (every_image>0)
|
||||
particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
|
||||
if (every_velocity>0)
|
||||
particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
if (every_force>0)
|
||||
particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
if (every_species>0)
|
||||
particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
|
||||
if (every_charge>0) {
|
||||
particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
if (author_name!=NULL) delete [] author_name;
|
||||
for (int i=0; i<3; i++) {
|
||||
delete [] boundary[i];
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::write_header(bigint nbig)
|
||||
{
|
||||
return;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::pack(tagint *ids)
|
||||
{
|
||||
int m,n;
|
||||
|
||||
tagint *tag = atom->tag;
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
int *species = atom->type;
|
||||
double *q = atom->q;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int dim=domain->dimension;
|
||||
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
|
||||
m = n = 0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (every_position>=0) {
|
||||
int ix = (image[i] & IMGMASK) - IMGMAX;
|
||||
int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
int iz = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
if (unwrap_flag == 1) {
|
||||
buf[m++] = (x[i][0] + ix * xprd);
|
||||
buf[m++] = (x[i][1] + iy * yprd);
|
||||
if (dim>2) buf[m++] = (x[i][2] + iz * zprd);
|
||||
} else {
|
||||
buf[m++] = x[i][0];
|
||||
buf[m++] = x[i][1];
|
||||
if (dim>2) buf[m++] = x[i][2];
|
||||
}
|
||||
if (every_image>=0) {
|
||||
buf[m++] = ix;
|
||||
buf[m++] = iy;
|
||||
if (dim>2) buf[m++] = iz;
|
||||
}
|
||||
}
|
||||
if (every_velocity>=0) {
|
||||
buf[m++] = v[i][0];
|
||||
buf[m++] = v[i][1];
|
||||
if (dim>2) buf[m++] = v[i][2];
|
||||
}
|
||||
if (every_force>=0) {
|
||||
buf[m++] = f[i][0];
|
||||
buf[m++] = f[i][1];
|
||||
if (dim>2) buf[m++] = f[i][2];
|
||||
}
|
||||
if (every_species>=0)
|
||||
buf[m++] = species[i];
|
||||
if (every_charge>=0)
|
||||
buf[m++] = q[i];
|
||||
ids[n++] = tag[i];
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::write_data(int n, double *mybuf)
|
||||
{
|
||||
// copy buf atom coords into global array
|
||||
|
||||
int m = 0;
|
||||
int dim = domain->dimension;
|
||||
int k = dim*ntotal;
|
||||
int k_image = dim*ntotal;
|
||||
int k_velocity = dim*ntotal;
|
||||
int k_force = dim*ntotal;
|
||||
int k_species = ntotal;
|
||||
int k_charge = ntotal;
|
||||
for (int i = 0; i < n; i++) {
|
||||
if (every_position>=0) {
|
||||
for (int j=0; j<dim; j++) {
|
||||
dump_position[k++] = mybuf[m++];
|
||||
}
|
||||
if (every_image>=0)
|
||||
for (int j=0; j<dim; j++) {
|
||||
dump_image[k_image++] = mybuf[m++];
|
||||
}
|
||||
}
|
||||
if (every_velocity>=0)
|
||||
for (int j=0; j<dim; j++) {
|
||||
dump_velocity[k_velocity++] = mybuf[m++];
|
||||
}
|
||||
if (every_force>=0)
|
||||
for (int j=0; j<dim; j++) {
|
||||
dump_force[k_force++] = mybuf[m++];
|
||||
}
|
||||
if (every_species>=0)
|
||||
dump_species[k_species++] = mybuf[m++];
|
||||
if (every_charge>=0)
|
||||
dump_charge[k_charge++] = mybuf[m++];
|
||||
ntotal++;
|
||||
}
|
||||
|
||||
// if last chunk of atoms in this snapshot, write global arrays to file
|
||||
|
||||
if (ntotal == natoms) {
|
||||
if (every_dump>0) {
|
||||
write_frame();
|
||||
ntotal = 0;
|
||||
} else {
|
||||
write_fixed_frame();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int DumpH5MD::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (strcmp(arg[0],"unwrap") == 0) {
|
||||
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
|
||||
if (strcmp(arg[1],"yes") == 0) unwrap_flag = 1;
|
||||
else if (strcmp(arg[1],"no") == 0) unwrap_flag = 0;
|
||||
else error->all(FLERR,"Illegal dump_modify command");
|
||||
return 2;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::write_frame()
|
||||
{
|
||||
int local_step;
|
||||
double local_time;
|
||||
double edges[3];
|
||||
local_step = update->ntimestep;
|
||||
local_time = local_step * update->dt;
|
||||
edges[0] = boxxhi - boxxlo;
|
||||
edges[1] = boxyhi - boxylo;
|
||||
edges[2] = boxzhi - boxzlo;
|
||||
if (every_position>0) {
|
||||
if (local_step % (every_position*every_dump) == 0) {
|
||||
h5md_append(particles_data.position, dump_position, local_step, local_time);
|
||||
h5md_append(particles_data.box_edges, edges, local_step, local_time);
|
||||
if (every_image>0)
|
||||
h5md_append(particles_data.image, dump_image, local_step, local_time);
|
||||
}
|
||||
} else {
|
||||
if (do_box) h5md_append(particles_data.box_edges, edges, local_step, local_time);
|
||||
}
|
||||
if (every_velocity>0 && local_step % (every_velocity*every_dump) == 0) {
|
||||
h5md_append(particles_data.velocity, dump_velocity, local_step, local_time);
|
||||
}
|
||||
if (every_force>0 && local_step % (every_force*every_dump) == 0) {
|
||||
h5md_append(particles_data.force, dump_force, local_step, local_time);
|
||||
}
|
||||
if (every_species>0 && local_step % (every_species*every_dump) == 0) {
|
||||
h5md_append(particles_data.species, dump_species, local_step, local_time);
|
||||
}
|
||||
if (every_charge>0 && local_step % (every_charge*every_dump) == 0) {
|
||||
h5md_append(particles_data.charge, dump_charge, local_step, local_time);
|
||||
}
|
||||
}
|
||||
|
||||
void DumpH5MD::write_fixed_frame()
|
||||
{
|
||||
double edges[3];
|
||||
int dims[2];
|
||||
char *boundary[3];
|
||||
hid_t a, s, t;
|
||||
herr_t status;
|
||||
|
||||
for (int i=0; i<3; i++) {
|
||||
boundary[i] = new char[9];
|
||||
if (domain->periodicity[i]==1) {
|
||||
strcpy(boundary[i], "periodic");
|
||||
} else {
|
||||
strcpy(boundary[i], "none");
|
||||
}
|
||||
}
|
||||
|
||||
dims[0] = natoms;
|
||||
dims[1] = domain->dimension;
|
||||
|
||||
edges[0] = boxxhi - boxxlo;
|
||||
edges[1] = boxyhi - boxylo;
|
||||
edges[2] = boxzhi - boxzlo;
|
||||
if (every_position==0) {
|
||||
particles_data.position = h5md_create_fixed_data_simple(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, dump_position);
|
||||
h5md_create_box(&particles_data, dims[1], boundary, false, edges, NULL);
|
||||
if (every_image==0)
|
||||
particles_data.image = h5md_create_fixed_data_simple(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, dump_image);
|
||||
}
|
||||
if (every_velocity==0)
|
||||
particles_data.velocity = h5md_create_fixed_data_simple(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, dump_velocity);
|
||||
if (every_force==0)
|
||||
particles_data.force = h5md_create_fixed_data_simple(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, dump_force);
|
||||
if (every_species==0)
|
||||
particles_data.species = h5md_create_fixed_data_simple(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, dump_species);
|
||||
if (every_charge==0) {
|
||||
particles_data.charge = h5md_create_fixed_data_simple(particles_data.group, "charge", 1, dims, H5T_NATIVE_INT, dump_charge);
|
||||
h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
|
||||
}
|
||||
|
||||
for (int i=0; i<3; i++) {
|
||||
delete [] boundary[i];
|
||||
}
|
||||
}
|
||||
|
||||
107
src/USER-H5MD/dump_h5md.h
Normal file
107
src/USER-H5MD/dump_h5md.h
Normal file
@ -0,0 +1,107 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
Contributing author: Pierre de Buyl (KU Leuven)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef DUMP_CLASS
|
||||
|
||||
DumpStyle(h5md,DumpH5MD)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_DUMP_H5MD_H
|
||||
#define LMP_DUMP_H5MD_H
|
||||
|
||||
#include "dump.h"
|
||||
#include "ch5md.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class DumpH5MD : public Dump {
|
||||
public:
|
||||
DumpH5MD(class LAMMPS *, int, char**);
|
||||
virtual ~DumpH5MD();
|
||||
|
||||
private:
|
||||
int natoms,ntotal;
|
||||
int nevery_save;
|
||||
int unwrap_flag; // 1 if atom coords are unwrapped, 0 if no
|
||||
h5md_file datafile;
|
||||
int datafile_from_dump;
|
||||
h5md_particles_group particles_data;
|
||||
char *author_name;
|
||||
|
||||
bool do_box;
|
||||
bool create_group;
|
||||
|
||||
// data arrays and intervals
|
||||
int every_dump;
|
||||
double *dump_position;
|
||||
int every_position;
|
||||
int *dump_image;
|
||||
int every_image;
|
||||
double *dump_velocity;
|
||||
int every_velocity;
|
||||
double *dump_force;
|
||||
int every_force;
|
||||
int *dump_species;
|
||||
int every_species;
|
||||
int *dump_charge;
|
||||
int every_charge;
|
||||
|
||||
void init_style();
|
||||
int modify_param(int, char **);
|
||||
void openfile();
|
||||
void write_header(bigint);
|
||||
void pack(tagint *);
|
||||
void write_data(int, double *);
|
||||
|
||||
void write_frame();
|
||||
void write_fixed_frame();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Invalid number of arguments in dump h5md
|
||||
|
||||
Make sure that each data item (position, etc.) is followed by a dump
|
||||
interval.
|
||||
|
||||
E: Dump h5md requires sorting by atom ID
|
||||
|
||||
Use the dump_modify sort command to enable this.
|
||||
|
||||
E: Cannot use variable every setting for dump xtc
|
||||
|
||||
The format of this file requires snapshots at regular intervals.
|
||||
|
||||
E: Cannot change dump_modify every for dump xtc
|
||||
|
||||
The frequency of writing dump xtc snapshots cannot be changed.
|
||||
|
||||
E: Cannot set file_from in dump h5md after box or create_group
|
||||
|
||||
The file_from option modifies the box and create_group options and
|
||||
they must appear after file_from if used.
|
||||
|
||||
*/
|
||||
Reference in New Issue
Block a user