14. lmfit
15. clFFT
16. Guidelines Support Library (GSL)
+17. P0009 reference implementation (Sandia Corporation)
Our chosen method for packaging distributions (CPack) only permits a
package to have a single license file, so we are unfortunately forced
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
--
+
+17. P0009 reference implementation (Sandia Corporation)
+=======================================================
+
+ Files: src/gromacs/mdspan/*
+
+ Kokkos v. 2.0
+ Copyright (2014) Sandia Corporation
+
+Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+the U.S. Government retains certain rights in this software.
+
+Kokkos is licensed under 3-clause BSD terms of use:
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+2. 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.
+
+3. Neither the name of the Corporation nor the names of the
+contributors may be used to endorse or promote products derived from
+this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "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 SANDIA CORPORATION OR THE
+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.
+
+Questions? Contact Christian R. Trott (crtrott@sandia.gov)
# GROMACS 2016 2
# GROMACS 2018 3
# GROMACS 2019 4
+# GROMACS 2020 5
# LIBRARY_SOVERSION_MINOR so minor version for the built libraries.
# Should be increased for each release that changes only the implementation.
# In GROMACS, the typical policy is to increase it for each patch version
# The GROMACS convention is that these are the version number of the next
# release that is going to be made from this branch.
-set(GMX_VERSION_MAJOR 2019)
+set(GMX_VERSION_MAJOR 2020)
set(GMX_VERSION_PATCH 0)
# The suffix, on the other hand, is used mainly for betas and release
# candidates, where it signifies the most recent such release from
# this branch; it will be empty before the first such release, as well
# as after the final release is out.
-set(GMX_VERSION_SUFFIX "-rc1")
+set(GMX_VERSION_SUFFIX "")
# Conventionally with libtool, any ABI change must change the major
# version number, the minor version number should change if it's just
# here. The important thing is to minimize the chance of third-party
# code being able to dynamically link with a version of libgromacs
# that might not work.
-set(LIBRARY_SOVERSION_MAJOR 4)
+set(LIBRARY_SOVERSION_MAJOR 5)
set(LIBRARY_SOVERSION_MINOR 0)
set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
-set(REGRESSIONTEST_BRANCH "refs/heads/release-2019")
+set(REGRESSIONTEST_BRANCH "refs/heads/master")
# Run the regressiontests packaging job with the correct pakage
# version string, and the release box checked, in order to have it
# build the regressiontests tarball with all the right naming. The
# naming affects the md5sum that has to go here, and if it isn't right
# release workflow will report a failure.
-set(REGRESSIONTEST_MD5SUM "69da7f6a5bfcdb38b202eb9f9df69d01" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
+set(REGRESSIONTEST_MD5SUM "3d06d41e07f523d70ae575b9ad75c670" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
how-to/visualize.rst
install-guide/index.rst
release-notes/index.rst
+ release-notes/highlights.rst
+ release-notes/features.rst
+ release-notes/performance.rst
+ release-notes/tools.rst
+ release-notes/bugs-fixed.rst
+ release-notes/removed-functionality.rst
+ release-notes/deprecated-functionality.rst
+ release-notes/portability.rst
+ release-notes/miscellaneous.rst
release-notes/2019/major/highlights.rst
release-notes/2019/major/features.rst
release-notes/2019/major/performance.rst
-.. _anticipated-changes:
-
Changes anticipated to GROMACS 2019 functionality
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
--- /dev/null
+Removed functionality
+^^^^^^^^^^^^^^^^^^^^^
+
+gmx anadock
+"""""""""""
+The gmx anadock tool was removed since it does not belong in gromacs
+(it analyzes AutoDock outputs).
+
+gmx dyndom
+""""""""""
+The gmx dyndom tool was removed since it does not belong in gromacs
+(it analyzes DynDom outputs).
+
+gmx morph
+"""""""""
+The gmx morph tool was removed since it yields non-physical structures
+that can easily be done by a script.
--- /dev/null
+Bugs fixed
+^^^^^^^^^^
--- /dev/null
+.. _anticipated-changes:
+
+Changes anticipated to |Gromacs| NEXT functionality
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Functionality deprecated in |Gromacs| NEXT
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Functionality deprecated in |Gromacs| 2019
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Generation of virtual sites to replace aromatic rings in standard residues
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+These are thought to produce artefacts under some circumstances
+(unpublished results), were never well tested, are not widely used,
+and we need to simplify pdb2gmx.
+
+``gmx mdrun -gcom``
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+This feature sometimes overrides the effects of various .mdp settings
+in a way that is difficult to understand and report. A user who wants
+to do communication between PP ranks less often should choose their
+``nst*`` mdp options accordingly.
+
+Benchmarking options only available with ``gmx benchmark``
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+Options such as ``-confout``, ``-resethway``, ``-resetstep`` are not
+intended for use by regular mdrun users, so making them only available
+with a dedicated tool is more clear. Also, this permits us to customize
+defaults for e.g. writing files at the end of a simulation part in ways
+that suit the respective mdrun and benchmark use cases, so ``-confout``
+will no longer be required.
+
+``gmx mdrun -nsteps``
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+The number of simulation steps described by the .tpr file can be
+changed with ``gmx convert-tpr``, or altered in .mdp file before the
+call to ``gmx grompp``. The convenience of this mdrun option was
+outweighted by the doubtful quality of its implementation, no clear
+record in the log file, and lack of maintenance.
+
+Functionality deprecated before |Gromacs| 2019
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+This functionality has been declared as deprecated in previous versions
+of |Gromacs|, but has not yet been removed.
+
+The group cutoff scheme
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+All remaining aspects of the group cutoff scheme will be removed, once
+a few remaining features (e.g. tabulated interactions, energy-group
+exclusions, and vacuum simulations) are available with the Verlet
+scheme. Deprecated in GROMACS 5.1
--- /dev/null
+New and improved features
+^^^^^^^^^^^^^^^^^^^^^^^^^
--- /dev/null
+Highlights
+^^^^^^^^^^
+
+|Gromacs| NEXT was released on INSERT DATE HERE. Patch releases may
+have been made since then, please use the updated versions! Here are
+some highlights of what you can expect, along with more detail in the
+links below!
+
+As always, we've got several useful performance improvements, with or
+without GPUs, all enabled and automated by default. We are extremely
+interested in your feedback on how well this worked on your
+simulations and hardware. They are:
+
+* Cool quotes autogenerator
functionality supported, whereas patch releases contain only fixes for
issues identified in the corresponding major releases.
-Two versions of |Gromacs| are under active maintenance, the 2019
-series and the 2018 series. In the latter, only highly conservative
+Two versions of |Gromacs| are under active maintenance, the NEXT
+series and the 2019 series. In the latter, only highly conservative
fixes will be made, and only to address issues that affect scientific
correctness. Naturally, some of those releases will be made after the
-year 2018 ends, but we keep 2018 in the name so users understand how
+year 2019 ends, but we keep 2018 in the name so users understand how
up to date their version is. Such fixes will also be incorporated into
-the 2019 release series, as appropriate. Around the time the 2020
-release is made, the 2018 series will no longer be maintained.
+the NEXT release series, as appropriate. Around the time the NEXT+1
+release is made, the 2019 series will no longer be maintained.
Where issue numbers are reported in these release notes, more details
can be found at https://redmine.gromacs.org at that issue number.
+|Gromacs| NEXT series
+---------------------
+
+.. toctree::
+ :maxdepth: 1
+
+ highlights
+ features
+ performance
+ tools
+ bugs-fixed
+ deprecated-functionality
+ removed-functionality
+ portability
+ miscellaneous
+
+
|Gromacs| 2019 series
---------------------
--- /dev/null
+Miscellaneous
+^^^^^^^^^^^^^
--- /dev/null
+Performance improvements
+^^^^^^^^^^^^^^^^^^^^^^^^
--- /dev/null
+Portability
+^^^^^^^^^^^
--- /dev/null
+Removed functionality
+^^^^^^^^^^^^^^^^^^^^^
--- /dev/null
+Improvements to |Gromacs| tools
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
# release string. For roadmap details, see https://redmine.gromacs.org/issues/2585
set(GMXAPI_MAJOR 0)
set(GMXAPI_MINOR 0)
-set(GMXAPI_PATCH 7)
+set(GMXAPI_PATCH 8)
set(GMXAPI_RELEASE ${GMXAPI_MAJOR}.${GMXAPI_MINOR}.${GMXAPI_PATCH})
###############################
* a microstate for gmxapi interfaces.
*/
- // Note: these output options normalize the file names, but not their
- // paths. gmxapi 0.0.7 changes working directory for each session, so the
- // relative paths are appropriate, but a near-future version will avoid
- // changing directories once the process starts and manage file paths explicitly.
- using gmxapi::c_majorVersion;
- using gmxapi::c_minorVersion;
- using gmxapi::c_patchVersion;
- static_assert(!(c_majorVersion != 0 || c_minorVersion != 0 || c_patchVersion > 7),
- "Developer notice: check assumptions about working directory and relative file paths for this "
- "software version.");
-
// Set input TPR name
mdArgs_.emplace_back("-s");
mdArgs_.emplace_back(filename);
+
// Set checkpoint file name
mdArgs_.emplace_back("-cpi");
mdArgs_.emplace_back("state.cpt");
+ /* Note: we normalize the checkpoint file name, but not its full path.
+ * Through version 0.0.8, gmxapi clients change working directory
+ * for each session, so relative path(s) below are appropriate.
+ * A future gmxapi version should avoid changing directories once the
+ * process starts and instead manage files (paths) in an absolute and
+ * immutable way, with abstraction provided through the Context chain-of-responsibility.
+ * TODO: API abstractions for initializing simulations that may be new or partially complete.
+ * Reference gmxapi milestone 13 at https://redmine.gromacs.org/issues/2585
+ */
// Create a mock argv. Note that argv[0] is expected to hold the program name.
const int offset = 1;
add_subdirectory(math)
add_subdirectory(mdrun)
add_subdirectory(mdrunutility)
+add_subdirectory(mdspan)
add_subdirectory(mdtypes)
add_subdirectory(onlinehelp)
add_subdirectory(options)
{
for (int atomIndex = 0; atomIndex < atoms.nr; atomIndex++, i++)
{
- if (getGroupType(&mtop->groups, gtype, i) != 0)
+ if (getGroupType(mtop->groups, gtype, i) != 0)
{
return FALSE;
}
char *res_name;
int res_id;
- if (getGroupType(&mtop->groups, egcCompressedX, i) != 0)
+ if (getGroupType(mtop->groups, egcCompressedX, i) != 0)
{
continue;
}
int atom1, atom2;
atom1 = ilist.iatoms[l] + atom_offset;
atom2 = ilist.iatoms[l + 1] + atom_offset;
- if (getGroupType(&mtop->groups, egcCompressedX, atom1) == 0 &&
- getGroupType(&mtop->groups, egcCompressedX, atom2) == 0)
+ if (getGroupType(mtop->groups, egcCompressedX, atom1) == 0 &&
+ getGroupType(mtop->groups, egcCompressedX, atom2) == 0)
{
tng_molecule_bond_add(tng, mol, ilist.iatoms[l],
ilist.iatoms[l + 1], &tngBond);
atom1 = ilist.iatoms[l] + atom_offset;
atom2 = ilist.iatoms[l + 1] + atom_offset;
atom3 = ilist.iatoms[l + 2] + atom_offset;
- if (getGroupType(&mtop->groups, egcCompressedX, atom1) == 0)
+ if (getGroupType(mtop->groups, egcCompressedX, atom1) == 0)
{
- if (getGroupType(&mtop->groups, egcCompressedX, atom2) == 0)
+ if (getGroupType(mtop->groups, egcCompressedX, atom2) == 0)
{
tng_molecule_bond_add(tng, mol, atom1,
atom2, &tngBond);
}
- if (getGroupType(&mtop->groups, egcCompressedX, atom3) == 0)
+ if (getGroupType(mtop->groups, egcCompressedX, atom3) == 0)
{
tng_molecule_bond_add(tng, mol, atom1,
atom3, &tngBond);
#ifndef _gmx_ana_h
#define _gmx_ana_h
-int
-gmx_anadock(int argc, char *argv[]);
-
int
gmx_analyze(int argc, char *argv[]);
int
gmx_dyecoupl(int argc, char *argv[]);
-int
-gmx_dyndom(int argc, char *argv[]);
-
int
gmx_editconf(int argc, char *argv[]);
int
gmx_msd(int argc, char *argv[]);
-int
-gmx_morph(int argc, char *argv[]);
-
int
gmx_nmeig(int argc, char *argv[]);
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
-
-#include <string>
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/statistics/statistics.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/arraysize.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/path.h"
-#include "gromacs/utility/pleasecite.h"
-#include "gromacs/utility/smalloc.h"
-
-static const char *etitles[] = { "E-docked", "Free Energy" };
-
-typedef struct {
- real edocked, efree;
- int index, cluster_id;
- t_atoms atoms;
- rvec *x;
- int ePBC;
- matrix box;
-} t_pdbfile;
-
-static t_pdbfile *read_pdbf(const char *fn)
-{
- t_pdbfile *pdbf;
- double e;
- FILE *fp;
-
- snew(pdbf, 1);
- t_topology top;
- read_tps_conf(fn, &top, &pdbf->ePBC, &pdbf->x, nullptr, pdbf->box, FALSE);
- pdbf->atoms = top.atoms;
- fp = gmx_ffopen(fn, "r");
- char buf[256], *ptr;
- while ((ptr = fgets2(buf, 255, fp)) != nullptr)
- {
- if (std::strstr(buf, "Intermolecular") != nullptr)
- {
- ptr = std::strchr(buf, '=');
- sscanf(ptr+1, "%lf", &e);
- pdbf->edocked = e;
- }
- else if (std::strstr(buf, "Estimated Free") != nullptr)
- {
- ptr = std::strchr(buf, '=');
- sscanf(ptr+1, "%lf", &e);
- pdbf->efree = e;
- }
- }
- gmx_ffclose(fp);
-
- return pdbf;
-}
-
-static t_pdbfile **read_em_all(const std::string &fn, int *npdbf)
-{
- t_pdbfile **pdbf = nullptr;
- int i, maxpdbf;
- gmx_bool bExist;
-
- maxpdbf = 100;
- snew(pdbf, maxpdbf);
- i = 0;
- do
- {
- auto newFilename = gmx::Path::concatenateBeforeExtension(fn, gmx::formatString("_%d", i+1));
- if ((bExist = gmx_fexist(newFilename)))
- {
- pdbf[i] = read_pdbf(newFilename.c_str());
- pdbf[i]->index = i+1;
- i++;
- if (i >= maxpdbf)
- {
- maxpdbf += 100;
- srenew(pdbf, maxpdbf);
- }
- }
- }
- while (bExist);
-
- *npdbf = i;
-
- printf("Found %d pdb files\n", i);
-
- return pdbf;
-}
-
-static gmx_bool bFreeSort = FALSE;
-
-static int pdbf_comp(const void *a, const void *b)
-{
- const t_pdbfile *pa, *pb;
- real x;
- int dc;
-
- pa = *static_cast<t_pdbfile *const*>(a);
- pb = *static_cast<t_pdbfile *const*>(b);
-
- dc = pa->cluster_id - pb->cluster_id;
-
- if (dc == 0)
- {
- if (bFreeSort)
- {
- x = pa->efree - pb->efree;
- }
- else
- {
- x = pa->edocked - pb->edocked;
- }
-
- if (x < 0)
- {
- return -1;
- }
- else if (x > 0)
- {
- return 1;
- }
- else
- {
- return 0;
- }
- }
- else
- {
- return dc;
- }
-}
-
-static void analyse_em_all(int npdb, t_pdbfile *pdbf[], const char *edocked,
- const char *efree, const gmx_output_env_t *oenv)
-{
- FILE *fp;
- int i;
-
- for (int freeSort = 0; freeSort < 2; freeSort++)
- {
- bFreeSort = (freeSort == 1);
- qsort(pdbf, npdb, sizeof(pdbf[0]), pdbf_comp);
- fp = xvgropen(bFreeSort ? efree : edocked,
- etitles[bFreeSort], "()", "E (kJ/mol)", oenv);
- for (i = 0; (i < npdb); i++)
- {
- fprintf(fp, "%12lf\n", bFreeSort ? pdbf[i]->efree : pdbf[i]->edocked);
- }
- xvgrclose(fp);
- }
-}
-
-static void clust_stat(FILE *fp, int start, int end, t_pdbfile *pdbf[])
-{
- int i;
- gmx_stats_t ed, ef;
- real aver, sigma;
-
- ed = gmx_stats_init();
- ef = gmx_stats_init();
- for (i = start; (i < end); i++)
- {
- gmx_stats_add_point(ed, i-start, pdbf[i]->edocked, 0, 0);
- gmx_stats_add_point(ef, i-start, pdbf[i]->efree, 0, 0);
- }
- gmx_stats_get_ase(ed, &aver, &sigma, nullptr);
- fprintf(fp, " <%12s> = %8.3f (+/- %6.3f)\n", etitles[FALSE], aver, sigma);
- gmx_stats_get_ase(ef, &aver, &sigma, nullptr);
- fprintf(fp, " <%12s> = %8.3f (+/- %6.3f)\n", etitles[TRUE], aver, sigma);
- gmx_stats_free(ed);
- gmx_stats_free(ef);
-}
-
-static real rmsd_dist(t_pdbfile *pa, t_pdbfile *pb, gmx_bool bRMSD)
-{
- int i;
- real rmsd;
- rvec acm, bcm, dx;
-
- if (bRMSD)
- {
- rmsd = 0;
- for (i = 0; (i < pa->atoms.nr); i++)
- {
- rvec_sub(pa->x[i], pb->x[i], dx);
- rmsd += iprod(dx, dx);
- }
- rmsd = std::sqrt(rmsd/pa->atoms.nr);
- }
- else
- {
- clear_rvec(acm);
- clear_rvec(bcm);
- for (i = 0; (i < pa->atoms.nr); i++)
- {
- rvec_inc(acm, pa->x[i]);
- rvec_inc(bcm, pb->x[i]);
- }
- rvec_sub(acm, bcm, dx);
- for (i = 0; (i < DIM); i++)
- {
- dx[i] /= pa->atoms.nr;
- }
- rmsd = norm(dx);
- }
- return rmsd;
-}
-
-static void line(FILE *fp)
-{
- fprintf(fp, " - - - - - - - - - -\n");
-}
-
-static void cluster_em_all(FILE *fp, int npdb, t_pdbfile *pdbf[],
- gmx_bool bFree, gmx_bool bRMSD, real cutoff)
-{
- int i, j, k;
- int *cndx, ncluster;
- real rmsd;
-
- bFreeSort = bFree;
- qsort(pdbf, npdb, sizeof(pdbf[0]), pdbf_comp);
-
- fprintf(fp, "Statistics over all structures:\n");
- clust_stat(fp, 0, npdb, pdbf);
- line(fp);
-
- /* Index to first structure in a cluster */
- snew(cndx, npdb);
- ncluster = 1;
-
- for (i = 1; (i < npdb); i++)
- {
- for (j = 0; (j < ncluster); j++)
- {
- rmsd = rmsd_dist(pdbf[cndx[j]], pdbf[i], bRMSD);
- if (rmsd <= cutoff)
- {
- /* Structure i is in cluster j */
- pdbf[i]->cluster_id = pdbf[cndx[j]]->cluster_id;
- break;
- }
- }
- if (j == ncluster)
- {
- /* New cluster! Cool! */
- cndx[ncluster] = i;
- pdbf[i]->cluster_id = ncluster;
- ncluster++;
- }
- }
- cndx[ncluster] = npdb;
- qsort(pdbf, npdb, sizeof(pdbf[0]), pdbf_comp);
-
- j = 0;
- cndx[j++] = 0;
- for (i = 1; (i < npdb); i++)
- {
- if (pdbf[i]->cluster_id != pdbf[i-1]->cluster_id)
- {
- cndx[j++] = i;
- }
- }
- cndx[j] = npdb;
- if (j != ncluster)
- {
- gmx_fatal(FARGS, "Consistency error: j = %d, ncluster = %d", j, ncluster);
- }
-
- fprintf(fp, "I found %d clusters based on %s and %s with a %.3f nm cut-off\n",
- ncluster, etitles[bFree], bRMSD ? "RMSD" : "distance", cutoff);
- line(fp);
- for (j = 0; (j < ncluster); j++)
- {
- fprintf(fp, "Cluster: %3d %s: %10.5f kJ/mol %3d elements\n",
- j, etitles[bFree],
- bFree ? pdbf[cndx[j]]->efree : pdbf[cndx[j]]->edocked,
- cndx[j+1]-cndx[j]);
- clust_stat(fp, cndx[j], cndx[j+1], pdbf);
- for (k = cndx[j]; (k < cndx[j+1]); k++)
- {
- fprintf(fp, " %3d", pdbf[k]->index);
- }
- fprintf(fp, "\n");
- line(fp);
- }
- sfree(cndx);
-}
-
-int gmx_anadock(int argc, char *argv[])
-{
- const char *desc[] = {
- "[THISMODULE] analyses the results of an Autodock run and clusters the",
- "structures together, based on distance or RMSD. The docked energy",
- "and free energy estimates are analysed, and for each cluster the",
- "energy statistics are printed.[PAR]",
- "An alternative approach to this is to cluster the structures first",
- "using [gmx-cluster] and then sort the clusters on either lowest",
- "energy or average energy."
- };
- t_filenm fnm[] = {
- { efPDB, "-f", nullptr, ffREAD },
- { efXVG, "-od", "edocked", ffWRITE },
- { efXVG, "-of", "efree", ffWRITE },
- { efLOG, "-g", "anadock", ffWRITE }
- };
- gmx_output_env_t *oenv;
-#define NFILE asize(fnm)
- static gmx_bool bFree = FALSE, bRMS = TRUE;
- static real cutoff = 0.2;
- t_pargs pa[] = {
- { "-free", FALSE, etBOOL, {&bFree},
- "Use Free energy estimate from autodock for sorting the classes" },
- { "-rms", FALSE, etBOOL, {&bRMS},
- "Cluster on RMS or distance" },
- { "-cutoff", FALSE, etREAL, {&cutoff},
- "Maximum RMSD/distance for belonging to the same cluster" }
- };
-#define NPA asize(pa)
-
- FILE *fp;
- t_pdbfile **pdbf = nullptr;
- int npdbf;
-
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
- nullptr, &oenv))
- {
- return 0;
- }
-
- fp = gmx_ffopen(opt2fn("-g", NFILE, fnm), "w");
- please_cite(stdout, "Hetenyi2002b");
- please_cite(fp, "Hetenyi2002b");
-
- pdbf = read_em_all(opt2fn("-f", NFILE, fnm), &npdbf);
-
- analyse_em_all(npdbf, pdbf, opt2fn("-od", NFILE, fnm), opt2fn("-of", NFILE, fnm),
- oenv);
-
- cluster_em_all(fp, npdbf, pdbf, bFree, bRMS, cutoff);
-
- gmx_ffclose(fp);
-
- return 0;
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include <cmath>
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/math/3dtransforms.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/atoms.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/arraysize.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
-static void rot_conf(t_atoms *atoms, const rvec x[], const rvec v[], real trans, real angle,
- rvec head, rvec tail, int isize, const int index[],
- rvec xout[], rvec vout[])
-{
- rvec arrow, xcm;
- real theta, phi, arrow_len;
- mat4 Rx, Ry, Rz, Rinvy, Rinvz, Mtot;
- mat4 temp1, temp2, temp3;
- vec4 xv;
- int i, ai;
-
- rvec_sub(tail, head, arrow);
- arrow_len = norm(arrow);
- if (debug)
- {
- fprintf(debug, "Arrow vector: %10.4f %10.4f %10.4f\n",
- arrow[XX], arrow[YY], arrow[ZZ]);
- fprintf(debug, "Effective translation %g nm\n", trans);
- }
- if (arrow_len == 0.0)
- {
- gmx_fatal(FARGS, "Arrow vector not given");
- }
-
- /* Copy all aoms to output */
- for (i = 0; (i < atoms->nr); i++)
- {
- copy_rvec(x[i], xout[i]);
- copy_rvec(v[i], vout[i]);
- }
-
- /* Compute center of mass and move atoms there */
- clear_rvec(xcm);
- for (i = 0; (i < isize); i++)
- {
- rvec_inc(xcm, x[index[i]]);
- }
- for (i = 0; (i < DIM); i++)
- {
- xcm[i] /= isize;
- }
- if (debug)
- {
- fprintf(debug, "Center of mass: %10.4f %10.4f %10.4f\n",
- xcm[XX], xcm[YY], xcm[ZZ]);
- }
- for (i = 0; (i < isize); i++)
- {
- rvec_sub(x[index[i]], xcm, xout[index[i]]);
- }
-
- /* Compute theta and phi that describe the arrow */
- theta = std::acos(arrow[ZZ]/arrow_len);
- phi = std::atan2(arrow[YY]/arrow_len, arrow[XX]/arrow_len);
- if (debug)
- {
- fprintf(debug, "Phi = %.1f, Theta = %.1f\n", RAD2DEG*phi, RAD2DEG*theta);
- }
-
- /* Now the total rotation matrix: */
- /* Rotate a couple of times */
- gmx_mat4_init_rotation(ZZ, -phi, Rz);
- gmx_mat4_init_rotation(YY, M_PI/2-theta, Ry);
- gmx_mat4_init_rotation(XX, angle*DEG2RAD, Rx);
- Rx[WW][XX] = trans;
- gmx_mat4_init_rotation(YY, theta-M_PI/2, Rinvy);
- gmx_mat4_init_rotation(ZZ, phi, Rinvz);
-
- gmx_mat4_mmul(temp1, Ry, Rz);
- gmx_mat4_mmul(temp2, Rinvy, Rx);
- gmx_mat4_mmul(temp3, temp2, temp1);
- gmx_mat4_mmul(Mtot, Rinvz, temp3);
-
- if (debug)
- {
- gmx_mat4_print(debug, "Rz", Rz);
- gmx_mat4_print(debug, "Ry", Ry);
- gmx_mat4_print(debug, "Rx", Rx);
- gmx_mat4_print(debug, "Rinvy", Rinvy);
- gmx_mat4_print(debug, "Rinvz", Rinvz);
- gmx_mat4_print(debug, "Mtot", Mtot);
- }
-
- for (i = 0; (i < isize); i++)
- {
- ai = index[i];
- gmx_mat4_transform_point(Mtot, xout[ai], xv);
- rvec_add(xv, xcm, xout[ai]);
- gmx_mat4_transform_point(Mtot, v[ai], xv);
- copy_rvec(xv, vout[ai]);
- }
-}
-
-int gmx_dyndom(int argc, char *argv[])
-{
- const char *desc[] = {
- "[THISMODULE] reads a [REF].pdb[ref] file output from DynDom",
- "(http://www.cmp.uea.ac.uk/dyndom/).",
- "It reads the coordinates, the coordinates of the rotation axis,",
- "and an index file containing the domains.",
- "Furthermore, it takes the first and last atom of the arrow file",
- "as command line arguments (head and tail) and",
- "finally it takes the translation vector (given in DynDom info file)",
- "and the angle of rotation (also as command line arguments). If the angle",
- "determined by DynDom is given, one should be able to recover the",
- "second structure used for generating the DynDom output.",
- "Because of limited numerical accuracy this should be verified by",
- "computing an all-atom RMSD (using [gmx-confrms]) rather than by file",
- "comparison (using diff).[PAR]",
- "The purpose of this program is to interpolate and extrapolate the",
- "rotation as found by DynDom. As a result unphysical structures with",
- "long or short bonds, or overlapping atoms may be produced. Visual",
- "inspection, and energy minimization may be necessary to",
- "validate the structure."
- };
- static real trans0 = 0;
- static rvec head = { 0, 0, 0 };
- static rvec tail = { 0, 0, 0 };
- static real angle0 = 0, angle1 = 0, maxangle = 0;
- static int label = 0, nframes = 11;
- t_pargs pa[] = {
- { "-firstangle", FALSE, etREAL, {&angle0},
- "Angle of rotation about rotation vector" },
- { "-lastangle", FALSE, etREAL, {&angle1},
- "Angle of rotation about rotation vector" },
- { "-nframe", FALSE, etINT, {&nframes},
- "Number of steps on the pathway" },
- { "-maxangle", FALSE, etREAL, {&maxangle},
- "DymDom dtermined angle of rotation about rotation vector" },
- { "-trans", FALSE, etREAL, {&trans0},
- "Translation (Angstrom) along rotation vector (see DynDom info file)" },
- { "-head", FALSE, etRVEC, {head},
- "First atom of the arrow vector" },
- { "-tail", FALSE, etRVEC, {tail},
- "Last atom of the arrow vector" }
- };
- int i, j, natoms, isize;
- t_trxstatus *status;
- int *index = nullptr, *index_all;
- char *grpname;
- real angle, trans;
- rvec *x, *v, *xout, *vout;
- matrix box;
- gmx_output_env_t *oenv;
-
- t_filenm fnm[] = {
- { efPDB, "-f", "dyndom", ffREAD },
- { efTRO, "-o", "rotated", ffWRITE },
- { efNDX, "-n", "domains", ffREAD }
- };
-#define NFILE asize(fnm)
-
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
- {
- return 0;
- }
-
- if (maxangle == 0)
- {
- gmx_fatal(FARGS, "maxangle not given");
- }
-
- t_topology *top;
- snew(top, 1);
- read_tps_conf(opt2fn("-f", NFILE, fnm), top, nullptr, &x, &v, box, FALSE);
- t_atoms &atoms = top->atoms;
- if (atoms.pdbinfo == nullptr)
- {
- snew(atoms.pdbinfo, atoms.nr);
- }
- atoms.havePdbInfo = TRUE;
- natoms = atoms.nr;
- snew(xout, natoms);
- snew(vout, natoms);
-
- printf("Select group to rotate:\n");
- rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
- printf("Going to rotate %s containing %d atoms\n", grpname, isize);
-
- snew(index_all, atoms.nr);
- for (i = 0; (i < atoms.nr); i++)
- {
- index_all[i] = i;
- }
-
- status = open_trx(opt2fn("-o", NFILE, fnm), "w");
-
- label = 'A';
- for (i = 0; (i < nframes); i++, label++)
- {
- angle = angle0 + (i*(angle1-angle0))/(nframes-1);
- trans = trans0*0.1*angle/maxangle;
- printf("Frame: %2d (label %c), angle: %8.3f deg., trans: %8.3f nm\n",
- i, label, angle, trans);
- rot_conf(&atoms, x, v, trans, angle, head, tail, isize, index, xout, vout);
-
- if (label > 'Z')
- {
- label -= 26;
- }
- for (j = 0; (j < atoms.nr); j++)
- {
- atoms.resinfo[atoms.atom[j].resind].chainid = label;
- }
-
- write_trx(status, atoms.nr, index_all, &atoms, i, angle, box, xout, vout, nullptr);
- }
- close_trx(status);
-
- return 0;
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/commandline/viewit.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/math/do_fit.h"
-#include "gromacs/topology/atoms.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/arraysize.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
-static real dointerp(int n, rvec x1[], rvec x2[], rvec xx[],
- int I, int N, real first, real last)
-{
- int i, j;
- double fac, fac0, fac1;
-
- fac = first + (I*(last-first))/(N-1);
- fac0 = 1-fac;
- fac1 = fac;
- for (i = 0; (i < n); i++)
- {
- for (j = 0; (j < DIM); j++)
- {
- xx[i][j] = fac0*x1[i][j] + fac1*x2[i][j];
- }
- }
-
- return fac;
-}
-
-int gmx_morph(int argc, char *argv[])
-{
- const char *desc[] = {
- "[THISMODULE] does a linear interpolation of conformations in order to",
- "create intermediates. Of course these are completely unphysical, but",
- "that you may try to justify yourself. Output is in the form of a ",
- "generic trajectory. The number of intermediates can be controlled with",
- "the [TT]-ninterm[tt] flag. The first and last flag correspond to the way of",
- "interpolating: 0 corresponds to input structure 1 while",
- "1 corresponds to input structure 2.",
- "If you specify [TT]-first[tt] < 0 or [TT]-last[tt] > 1 extrapolation will be",
- "on the path from input structure x[SUB]1[sub] to x[SUB]2[sub]. In general, the coordinates",
- "of the intermediate x(i) out of N total intermediates correspond to:[PAR]",
- "x(i) = x[SUB]1[sub] + (first+(i/(N-1))*(last-first))*(x[SUB]2[sub]-x[SUB]1[sub])[PAR]",
- "Finally the RMSD with respect to both input structures can be computed",
- "if explicitly selected ([TT]-or[tt] option). In that case, an index file may be",
- "read to select the group from which the RMS is computed."
- };
- t_filenm fnm[] = {
- { efSTX, "-f1", "conf1", ffREAD },
- { efSTX, "-f2", "conf2", ffREAD },
- { efTRX, "-o", "interm", ffWRITE },
- { efXVG, "-or", "rms-interm", ffOPTWR },
- { efNDX, "-n", "index", ffOPTRD }
- };
-#define NFILE asize(fnm)
- static int ninterm = 11;
- static real first = 0.0;
- static real last = 1.0;
- static gmx_bool bFit = TRUE;
- t_pargs pa [] = {
- { "-ninterm", FALSE, etINT, {&ninterm},
- "Number of intermediates" },
- { "-first", FALSE, etREAL, {&first},
- "Corresponds to first generated structure (0 is input x[SUB]1[sub], see above)" },
- { "-last", FALSE, etREAL, {&last},
- "Corresponds to last generated structure (1 is input x[SUB]2[sub], see above)" },
- { "-fit", FALSE, etBOOL, {&bFit},
- "Do a least squares fit of the second to the first structure before interpolating" }
- };
- const char *leg[] = { "Ref = 1\\Sst\\N conf", "Ref = 2\\Snd\\N conf" };
- FILE *fp = nullptr;
- int i, isize, is_lsq, nat1, nat2;
- t_trxstatus *status;
- int *index, *index_lsq, *index_all, *dummy;
- rvec *x1, *x2, *xx;
- matrix box;
- real rms1, rms2, fac, *mass;
- char *grpname;
- gmx_bool bRMS;
- gmx_output_env_t *oenv;
-
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, nullptr, &oenv))
- {
- return 0;
- }
-
- t_topology *top;
- snew(top, 1);
- read_tps_conf(opt2fn("-f1", NFILE, fnm), top, nullptr, &x1, nullptr, box, FALSE);
- nat1 = top->atoms.nr;
- read_tps_conf(opt2fn("-f2", NFILE, fnm), top, nullptr, &x2, nullptr, box, FALSE);
- nat2 = top->atoms.nr;
- if (nat1 != nat2)
- {
- gmx_fatal(FARGS, "Number of atoms in first structure is %d, in second %d",
- nat1, nat2);
- }
- snew(xx, nat1);
- t_atoms &atoms = top->atoms;
-
- snew(mass, nat1);
- snew(index_all, nat1);
- for (i = 0; (i < nat1); i++)
- {
- mass[i] = 1;
- index_all[i] = i;
- }
- if (bFit)
- {
- printf("Select group for LSQ superposition:\n");
- get_index(&atoms, opt2fn_null("-n", NFILE, fnm), 1, &is_lsq, &index_lsq,
- &grpname);
- reset_x(is_lsq, index_lsq, nat1, index_all, x1, mass);
- reset_x(is_lsq, index_lsq, nat1, index_all, x2, mass);
- do_fit(nat1, mass, x1, x2);
- }
-
- bRMS = opt2bSet("-or", NFILE, fnm);
- if (bRMS)
- {
- fp = xvgropen(opt2fn("-or", NFILE, fnm), "RMSD", "Conf", "(nm)", oenv);
- xvgr_legend(fp, asize(leg), leg, oenv);
- printf("Select group for RMSD calculation:\n");
- get_index(&atoms, opt2fn_null("-n", NFILE, fnm), 1, &isize, &index, &grpname);
- printf("You selected group %s, containing %d atoms\n", grpname, isize);
- rms1 = rmsdev_ind(isize, index, mass, x1, x2);
- fprintf(stderr, "RMSD between input conformations is %g nm\n", rms1);
- }
-
- snew(dummy, nat1);
- for (i = 0; (i < nat1); i++)
- {
- dummy[i] = i;
- }
- status = open_trx(ftp2fn(efTRX, NFILE, fnm), "w");
-
- for (i = 0; (i < ninterm); i++)
- {
- fac = dointerp(nat1, x1, x2, xx, i, ninterm, first, last);
- write_trx(status, nat1, dummy, &atoms, i, fac, box, xx, nullptr, nullptr);
- if (bRMS)
- {
- rms1 = rmsdev_ind(isize, index, mass, x1, xx);
- rms2 = rmsdev_ind(isize, index, mass, x2, xx);
- fprintf(fp, "%10g %10g %10g\n", fac, rms1, rms2);
- }
- }
-
- close_trx(status);
-
- if (bRMS)
- {
- xvgrclose(fp);
- do_view(oenv, opt2fn("-or", NFILE, fnm), "-nxy");
- }
-
- return 0;
-}
#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
+#include "gromacs/compat/make_unique.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
NOT_USED, NORMAL, X, Y, Z, LATERAL
} msd_type;
-typedef struct {
+struct t_corr {
real t0; /* start time and time increment between */
real delta_t; /* time between restart points */
real beginfit, /* the begin/end time for fits as reals between */
int *n_offs;
int **ndata; /* the number of msds (particles/mols) per data
point. */
-} t_corr;
-
-typedef real t_calc_func (t_corr *curr, int nx, const int index[], int nx0, rvec xc[],
- const rvec dcom, gmx_bool bTen, matrix mat);
-
-static real thistime(t_corr *curr)
-{
- return curr->time[curr->nframes];
-}
-
-static int in_data(t_corr *curr, int nx00)
-{
- return curr->nframes-curr->n_offs[nx00];
-}
-
-static t_corr *init_corr(int nrgrp, int type, int axis, real dim_factor,
- int nmol, gmx_bool bTen, gmx_bool bMass, real dt, const t_topology *top,
- real beginfit, real endfit)
-{
- t_corr *curr;
- int i;
-
- snew(curr, 1);
- curr->type = static_cast<msd_type>(type);
- curr->axis = axis;
- curr->ngrp = nrgrp;
- curr->nrestart = 0;
- curr->delta_t = dt;
- curr->beginfit = (1 - 2*GMX_REAL_EPS)*beginfit;
- curr->endfit = (1 + 2*GMX_REAL_EPS)*endfit;
- curr->x0 = nullptr;
- curr->n_offs = nullptr;
- curr->nframes = 0;
- curr->nlast = 0;
- curr->dim_factor = dim_factor;
-
- snew(curr->ndata, nrgrp);
- snew(curr->data, nrgrp);
- if (bTen)
+ t_corr(int nrgrp, int type, int axis, real dim_factor, int nmol,
+ gmx_bool bTen, gmx_bool bMass, real dt, const t_topology *top,
+ real beginfit, real endfit) :
+ t0(0),
+ delta_t(dt),
+ beginfit((1 - 2*GMX_REAL_EPS)*beginfit),
+ endfit((1 + 2*GMX_REAL_EPS)*endfit),
+ dim_factor(dim_factor),
+ data(nullptr),
+ time(nullptr),
+ mass(nullptr),
+ datam(nullptr),
+ x0(nullptr),
+ com(nullptr),
+ lsq(nullptr),
+ type(static_cast<msd_type>(type)),
+ axis(axis),
+ ncoords(0),
+ nrestart(0),
+ nmol(nmol),
+ nframes(0),
+ nlast(0),
+ ngrp(nrgrp),
+ n_offs(nullptr),
+ ndata(nullptr)
{
- snew(curr->datam, nrgrp);
- }
- for (i = 0; (i < nrgrp); i++)
- {
- curr->ndata[i] = nullptr;
- curr->data[i] = nullptr;
+ snew(ndata, nrgrp);
+ snew(data, nrgrp);
if (bTen)
{
- curr->datam[i] = nullptr;
+ snew(datam, nrgrp);
}
- }
- curr->time = nullptr;
- curr->lsq = nullptr;
- curr->nmol = nmol;
- if (curr->nmol > 0)
- {
- snew(curr->mass, curr->nmol);
- for (i = 0; i < curr->nmol; i++)
+ for (int i = 0; (i < nrgrp); i++)
+ {
+ ndata[i] = nullptr;
+ data[i] = nullptr;
+ if (bTen)
+ {
+ datam[i] = nullptr;
+ }
+ }
+ if (nmol > 0)
{
- curr->mass[i] = 1;
+ snew(mass, nmol);
+ for (int i = 0; i < nmol; i++)
+ {
+ mass[i] = 1;
+ }
}
- }
- else
- {
- if (bMass)
+ else
{
- const t_atoms *atoms = &top->atoms;
- snew(curr->mass, atoms->nr);
- for (i = 0; (i < atoms->nr); i++)
+ if (bMass)
{
- curr->mass[i] = atoms->atom[i].m;
+ const t_atoms *atoms = &top->atoms;
+ snew(mass, atoms->nr);
+ for (int i = 0; (i < atoms->nr); i++)
+ {
+ mass[i] = atoms->atom[i].m;
+ }
}
}
}
+};
- return curr;
+typedef real t_calc_func (t_corr *curr, int nx, const int index[], int nx0, rvec xc[],
+ const rvec dcom, gmx_bool bTen, matrix mat);
+
+static real thistime(t_corr *curr)
+{
+ return curr->time[curr->nframes];
+}
+
+static int in_data(t_corr *curr, int nx00)
+{
+ return curr->nframes-curr->n_offs[nx00];
}
static void corr_print(t_corr *curr, gmx_bool bTen, const char *fn, const char *title,
int type, real dim_factor, int axis,
real dt, real beginfit, real endfit, const gmx_output_env_t *oenv)
{
- t_corr *msd;
- int *gnx; /* the selected groups' sizes */
- int **index; /* selected groups' indices */
- char **grpname;
- int i, i0, i1, j, N, nat_trx;
- real *DD, *SigmaD, a, a2, b, r, chi2;
- rvec *x = nullptr;
- matrix box;
- int *gnx_com = nullptr; /* the COM removal group size */
- int **index_com = nullptr; /* the COM removal group atom indices */
- char **grpname_com = nullptr; /* the COM removal group name */
+ std::unique_ptr<t_corr> msd;
+ int *gnx; /* the selected groups' sizes */
+ int **index; /* selected groups' indices */
+ char **grpname;
+ int i, i0, i1, j, N, nat_trx;
+ real *DD, *SigmaD, a, a2, b, r, chi2;
+ rvec *x = nullptr;
+ matrix box;
+ int *gnx_com = nullptr; /* the COM removal group size */
+ int **index_com = nullptr; /* the COM removal group atom indices */
+ char **grpname_com = nullptr; /* the COM removal group name */
snew(gnx, nrgrp);
snew(index, nrgrp);
index_atom2mol(&gnx[0], index[0], &top->mols);
}
- msd = init_corr(nrgrp, type, axis, dim_factor,
- mol_file == nullptr ? 0 : gnx[0], bTen, bMW, dt, top,
- beginfit, endfit);
+ msd = gmx::compat::make_unique<t_corr>(nrgrp, type, axis, dim_factor,
+ mol_file == nullptr ? 0 : gnx[0],
+ bTen, bMW, dt, top, beginfit, endfit);
nat_trx =
- corr_loop(msd, trx_file, top, ePBC, mol_file ? gnx[0] != 0 : false, gnx, index,
+ corr_loop(msd.get(), trx_file, top, ePBC, mol_file ? gnx[0] != 0 : false, gnx, index,
(mol_file != nullptr) ? calc1_mol : (bMW ? calc1_mw : calc1_norm),
bTen, gnx_com, index_com, dt, t_pdb,
pdb_file ? &x : nullptr, box, oenv);
{
snew(top->atoms.pdbinfo, top->atoms.nr);
}
- printmol(msd, mol_file, pdb_file, index[0], top, x, ePBC, box, oenv);
+ printmol(msd.get(), mol_file, pdb_file, index[0], top, x, ePBC, box, oenv);
top->atoms.nr = i;
}
}
}
/* Print mean square displacement */
- corr_print(msd, bTen, msd_file,
+ corr_print(msd.get(), bTen, msd_file,
"Mean Square Displacement",
"MSD (nm\\S2\\N)",
msd->time[msd->nframes-1], beginfit, endfit, DD, SigmaD, grpname, oenv);
{
/* Get the energy group of the first atom in this charge group */
firstj = astart + molt->cgs.index[cg];
- firsteg = getGroupType(&mtop->groups, egcENER, firstj);
+ firsteg = getGroupType(mtop->groups, egcENER, firstj);
for (j = molt->cgs.index[cg]+1; j < molt->cgs.index[cg+1]; j++)
{
- eg = getGroupType(&mtop->groups, egcENER, astart+j);
+ eg = getGroupType(mtop->groups, egcENER, astart+j);
if (eg != firsteg)
{
gmx_fatal(FARGS, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
static void calc_nrdf(const gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
{
t_grpopts *opts;
- const gmx_groups_t *groups;
pull_params_t *pull;
int natoms, ai, aj, i, j, d, g, imin, jmin;
int *nrdf2, *na_vcm, na_tot;
opts = &ir->opts;
- groups = &mtop->groups;
+ const gmx_groups_t &groups = mtop->groups;
natoms = mtop->natoms;
/* Allocate one more for a possible rest group */
/* We need to sum degrees of freedom into doubles,
* since floats give too low nrdf's above 3 million atoms.
*/
- snew(nrdf_tc, groups->grps[egcTC].nr+1);
- snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
- snew(dof_vcm, groups->grps[egcVCM].nr+1);
- snew(na_vcm, groups->grps[egcVCM].nr+1);
- snew(nrdf_vcm_sub, groups->grps[egcVCM].nr+1);
+ snew(nrdf_tc, groups.grps[egcTC].nr+1);
+ snew(nrdf_vcm, groups.grps[egcVCM].nr+1);
+ snew(dof_vcm, groups.grps[egcVCM].nr+1);
+ snew(na_vcm, groups.grps[egcVCM].nr+1);
+ snew(nrdf_vcm_sub, groups.grps[egcVCM].nr+1);
- for (i = 0; i < groups->grps[egcTC].nr; i++)
+ for (i = 0; i < groups.grps[egcTC].nr; i++)
{
nrdf_tc[i] = 0;
}
- for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
+ for (i = 0; i < groups.grps[egcVCM].nr+1; i++)
{
nrdf_vcm[i] = 0;
clear_ivec(dof_vcm[i]);
nrdf_vcm[getGroupType(groups, egcVCM, ai)] -= 0.5*imin;
if (nrdf_tc[getGroupType(groups, egcTC, ai)] < 0)
{
- gmx_fatal(FARGS, "Center of mass pulling constraints caused the number of degrees of freedom for temperature coupling group %s to be negative", gnames[groups->grps[egcTC].nm_ind[getGroupType(groups, egcTC, ai)]]);
+ gmx_fatal(FARGS, "Center of mass pulling constraints caused the number of degrees of freedom for temperature coupling group %s to be negative", gnames[groups.grps[egcTC].nm_ind[getGroupType(groups, egcTC, ai)]]);
}
}
else
* the number of degrees of freedom in each vcm group when COM
* translation is removed and 6 when rotation is removed as well.
*/
- for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
+ for (j = 0; j < groups.grps[egcVCM].nr+1; j++)
{
switch (ir->comm_mode)
{
}
}
- for (i = 0; i < groups->grps[egcTC].nr; i++)
+ for (i = 0; i < groups.grps[egcTC].nr; i++)
{
/* Count the number of atoms of TC group i for every VCM group */
- for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
+ for (j = 0; j < groups.grps[egcVCM].nr+1; j++)
{
na_vcm[j] = 0;
}
*/
nrdf_uc = nrdf_tc[i];
nrdf_tc[i] = 0;
- for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
+ for (j = 0; j < groups.grps[egcVCM].nr+1; j++)
{
if (nrdf_vcm[j] > nrdf_vcm_sub[j])
{
}
}
}
- for (i = 0; (i < groups->grps[egcTC].nr); i++)
+ for (i = 0; (i < groups.grps[egcTC].nr); i++)
{
opts->nrdf[i] = nrdf_tc[i];
if (opts->nrdf[i] < 0)
}
fprintf(stderr,
"Number of degrees of freedom in T-Coupling group %s is %.2f\n",
- gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
+ gnames[groups.grps[egcTC].nm_ind[i]], opts->nrdf[i]);
}
sfree(nrdf2);
const t_atom *atom;
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
- mgrp[getGroupType(&sys->groups, egcACC, i)] += atom->m;
+ mgrp[getGroupType(sys->groups, egcACC, i)] += atom->m;
}
mt = 0.0;
for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
"solvate", "-cs"
};
setInputFile("-cp", "spc-and-methanol.gro");
-
- // TODO: Consider adding a convenience method for this.
- std::string topFileName = gmx::test::TestFileManager::getInputFilePath("spc-and-methanol.top");
- std::string modifiableTopFileName = fileManager().getTemporaryFilePath(".top");
- gmx_file_copy(topFileName.c_str(), modifiableTopFileName.c_str(), true);
- commandLine().addOption("-p", modifiableTopFileName);
+ setModifiableInputFile("-p", "spc-and-methanol.top");
runTest(CommandLine(cmdline));
}
};
setInputFile("-cs", "mixed_solvent.gro");
setInputFile("-cp", "simple.gro");
-
- // TODO: Consider adding a convenience method for this.
- // Copies topology file to where it would be found as an output file, so the copied
- // .top file is used as both input and output
- std::string topFileName = gmx::test::TestFileManager::getInputFilePath("simple.top");
- std::string modifiableTopFileName = fileManager().getTemporaryFilePath("simple.top");
- gmx_file_copy(topFileName.c_str(), modifiableTopFileName.c_str(), true);
- setOutputFile("-p", "simple.top", ExactTextMatch());
+ setInputAndOutputFile("-p", "simple.top", ExactTextMatch());
runTest(CommandLine(cmdline));
}
od->nref = 0;
for (int i = 0; i < mtop->natoms; i++)
{
- if (getGroupType(&mtop->groups, egcORFIT, i) == 0)
+ if (getGroupType(mtop->groups, egcORFIT, i) == 0)
{
od->nref++;
}
{
a0 = cgs->index[cg];
a1 = cgs->index[cg+1];
- if (getGroupType(&mtop->groups, egcENER, a_offset+am+a0) !=
- getGroupType(&mtop->groups, egcENER, a_offset +a0))
+ if (getGroupType(mtop->groups, egcENER, a_offset+am+a0) !=
+ getGroupType(mtop->groups, egcENER, a_offset +a0))
{
bId = FALSE;
}
a1 = cgs->index[cg+1];
/* Store the energy group in cginfo */
- gid = getGroupType(&mtop->groups, egcENER, a_offset+am+a0);
+ gid = getGroupType(mtop->groups, egcENER, a_offset+am+a0);
SET_CGINFO_GID(cginfo[cgm+cg], gid);
/* Check the intra/inter charge group exclusions */
md->bVCMgrps = FALSE;
for (int i = 0; i < mtop.natoms; i++)
{
- if (getGroupType(&mtop.groups, egcVCM, i) > 0)
+ if (getGroupType(mtop.groups, egcVCM, i) > 0)
{
md->bVCMgrps = TRUE;
}
{
gmx_bool bLJPME;
const t_grpopts *opts;
- const gmx_groups_t *groups;
int nthreads gmx_unused;
bLJPME = EVDW_PME(ir->vdwtype);
opts = &ir->opts;
- groups = &mtop->groups;
+ const gmx_groups_t &groups = mtop->groups;
- auto md = mdAtoms->mdatoms();
+ auto md = mdAtoms->mdatoms();
/* nindex>=0 indicates DD where we use an index */
if (nindex >= 0)
{
else
{
/* The friction coefficient is mass/tau_t */
- fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
+ fac = ir->delta_t/opts->tau_t[md->cTC ? groups.grpnr[egcTC][ag] : 0];
mA = 0.5*atom.m*fac;
mB = 0.5*atom.mB*fac;
}
md->ptype[i] = atom.ptype;
if (md->cTC)
{
- md->cTC[i] = groups->grpnr[egcTC][ag];
+ md->cTC[i] = groups.grpnr[egcTC][ag];
}
md->cENER[i] = getGroupType(groups, egcENER, ag);
if (md->cACC)
{
- md->cACC[i] = groups->grpnr[egcACC][ag];
+ md->cACC[i] = groups.grpnr[egcACC][ag];
}
if (md->cVCM)
{
- md->cVCM[i] = groups->grpnr[egcVCM][ag];
+ md->cVCM[i] = groups.grpnr[egcVCM][ag];
}
if (md->cORF)
{
if (md->cU1)
{
- md->cU1[i] = groups->grpnr[egcUser1][ag];
+ md->cU1[i] = groups.grpnr[egcUser1][ag];
}
if (md->cU2)
{
- md->cU2[i] = groups->grpnr[egcUser2][ag];
+ md->cU2[i] = groups.grpnr[egcUser2][ag];
}
if (ir->bQMMM)
{
- if (groups->grpnr[egcQMMM] == nullptr ||
- groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1)
+ if (groups.grpnr[egcQMMM] == nullptr ||
+ groups.grpnr[egcQMMM][ag] < groups.grps[egcQMMM].nr-1)
{
md->bQM[i] = TRUE;
}
of->natoms_x_compressed = 0;
for (i = 0; (i < top_global->natoms); i++)
{
- if (getGroupType(of->groups, egcCompressedX, i) == 0)
+ if (getGroupType(*of->groups, egcCompressedX, i) == 0)
{
of->natoms_x_compressed++;
}
auto x = makeArrayRef(state_global->x);
for (i = 0, j = 0; (i < of->natoms_global); i++)
{
- if (getGroupType(of->groups, egcCompressedX, i) == 0)
+ if (getGroupType(*of->groups, egcCompressedX, i) == 0)
{
copy_rvec(x[i], xxtc[j++]);
}
void done_ns(gmx_ns_t *ns, int numEnergyGroups)
{
+ if (ns->bexcl != nullptr)
+ {
+ sfree(ns->bexcl);
+ }
sfree(ns->bExcludeAlleg);
if (ns->ns_buf)
{
}
sfree(ns->ns_buf);
}
+ if (ns->nl_sr != nullptr)
+ {
+ for (int i = 0; i < numEnergyGroups; i++)
+ {
+ if (ns->nl_sr[i] != nullptr)
+ {
+ sfree(ns->nl_sr[i]);
+ }
+ }
+ sfree(ns->nl_sr);
+ }
sfree(ns->simple_aaj);
sfree(ns->bHaveVdW);
+ sfree(ns->nsr);
done_grid(ns->grid);
sfree(ns);
}
qr->nrQMlayers = 1;
}
- const gmx_groups_t *groups = &mtop->groups;
+ const gmx_groups_t &groups = mtop->groups;
/* there are jmax groups of QM atoms. In case of multiple QM groups
* I assume that the users wants to do ONIOM. However, maybe it
static void init_grpstat(const gmx_mtop_t *mtop, int ngacc, t_grp_acc gstat[])
{
- const gmx_groups_t *groups;
gmx_mtop_atomloop_all_t aloop;
int i, grp;
const t_atom *atom;
if (ngacc > 0)
{
- groups = &mtop->groups;
+ const gmx_groups_t &groups = mtop->groups;
aloop = gmx_mtop_atomloop_all_init(mtop);
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
destroy_enerdata(enerd);
+
sfree(enerd);
+
+ /* Clean up topology. top->atomtypes has an allocated pointer if no domain decomposition*/
+ if (!DOMAINDECOMP(cr))
+ {
+ done_atomtypes(&top->atomtypes);
+ }
sfree(top);
}
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2018, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+if (BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
--- /dev/null
+This directory contains a stripped-down and modified-for-GROMACS version
+of a reference implementation of the LEWG P0009 proposal, revision 8:
+"mdspan: A Non-Owning Multidimensional Array Reference"
+
+The full version is available from
+https://github.com/ORNL/cpp-proposals-pub/tree/master/P0009
+SHA1 of the commit used is f433984ba897298069b510aa1311145040dd860c.
+
+This work orginated from "Kokkos" and is distributed under the BSD license as
+stated in COPYING.
+
+The following modifications were carried out:
+* reformatted code with uncrustify
+* added GROMACS header to all files
+* added doxygen comments to all files
+* temporarily removed constexpr from functions, so they compile with C++11
+* put all headers from bits/ into this directory
+* use minimial includes in all header files instead of just including mdspan
+* move tests into a subdirectory tests and rename test_foo.cpp to foo.cpp
+* renamed tests and test fixture class to match GROMACS conventions
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*
+ * This file is a modified version of original work of Sandia Corporation.
+ * In the spirit of the original code, this particular file can be distributed
+ * on the terms of Sandia Corporation.
+ */
+/*
+ * Kokkos v. 2.0
+ * Copyright (2014) Sandia Corporation
+ *
+ * Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+ * the U.S. Government retains certain rights in this software.
+ *
+ * Kokkos is licensed under 3-clause BSD terms of use:
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are
+ * met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * 2. 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.
+ *
+ * 3. Neither the name of the Corporation nor the names of the
+ * contributors may be used to endorse or promote products derived from
+ * this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "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 SANDIA CORPORATION OR THE
+ * 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.
+ *
+ * Questions? Contact Christian R. Trott (crtrott@sandia.gov)
+ */
+/*! \libinternal \file
+ * \brief Declares gmx::extents for mdspan.
+ *
+ * \author Christian Trott <crtrott@sandia.gov>
+ * \author Ronan Keryell <ronan.keryell@xilinx.com>
+ * \author Carter Edwards <hedwards@nvidia.com>
+ * \author David Hollman <dshollm@sandia.gov>
+ * \author Christian Blau <cblau@gwdg.de>
+ * \ingroup mdspan
+ */
+#ifndef MDSPAN_EXTENTS_H
+#define MDSPAN_EXTENTS_H
+
+#include <cstddef>
+
+#include <array>
+
+namespace gmx
+{
+
+/*! \brief Define constant that signals dynamic extent.
+ */
+enum : std::ptrdiff_t {
+ dynamic_extent = -1
+};
+
+template< std::ptrdiff_t ... StaticExtents >
+class extents;
+
+template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
+bool operator==(const extents<LHS...> &lhs,
+ const extents<RHS...> &rhs) noexcept;
+
+template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
+constexpr bool operator!=(const extents<LHS...> &lhs,
+ const extents<RHS...> &rhs) noexcept;
+
+namespace detail
+{
+
+template< int R, std::ptrdiff_t ... StaticExtents >
+struct extents_analyse;
+
+/*! \libinternal \brief Enable querying extent of specific rank by splitting
+ * a static extents off the variadic template arguments.
+ *
+ */
+template< int R, std::ptrdiff_t E0, std::ptrdiff_t ... StaticExtents >
+struct extents_analyse<R, E0, StaticExtents...> {
+
+ //! The extent analysis of the next lower rank.
+ using next_extents_analyse = extents_analyse<R-1, StaticExtents...>;
+
+ /*! \brief Accumulate the total rank from all extents.
+ * \returns incremented rank of the next extent
+ */
+ static constexpr std::size_t rank() noexcept { return next_extents_analyse::rank()+1; }
+ /*! \brief Accumulate the dynamic rank from all extents.
+ * This extent is static, so hand down query to the next extent analysis.
+ * \returns the dynamic rank of the next extent analysis.
+ */
+ static constexpr std::size_t rank_dynamic() noexcept { return next_extents_analyse::rank_dynamic(); }
+
+ //! Store analysis of the next extent of next lower rank.
+ next_extents_analyse next;
+
+ //! Trivial constructor.
+ extents_analyse() : next() {}
+
+ /*! \brief Construction from dynamic extents hands the extents down
+ * to the next extents analysis of lower rank.
+ * \param[in] de dynamic extents
+ */
+ template<class ... DynamicExtents>
+ extents_analyse(DynamicExtents... de) : next(de ...) {}
+
+ /*! \brief Construct from an array of dynamic extentes and rank.
+ * Hand down the dynamic rank parameters to the next extents analysis rank
+ * \param[in] de dynamic extents
+ * \param[in] r rank to read from the dynamic extent
+ */
+ template<std::size_t Rank>
+ extents_analyse(const std::array<std::ptrdiff_t, Rank> &de, const std::size_t r) : next(de, r) {}
+
+ //! Copy constructor.
+ template<std::ptrdiff_t... OtherStaticExtents>
+ extents_analyse(extents_analyse<R, OtherStaticExtents...> rhs) : next(rhs.next) {}
+
+ //! Assignment operator.
+ template<std::ptrdiff_t... OtherStaticExtents>
+ extents_analyse &operator= (extents_analyse<R, OtherStaticExtents...> rhs)
+ {
+ next = rhs.next;
+ return *this;
+ }
+
+ /*! \brief Report extent of dimension r.
+ * \param[in] r the dimension to query
+ * \returns the extent in dimension r.
+ */
+ constexpr std::ptrdiff_t extent(const std::size_t r) const noexcept
+ {
+ // TODO use early return and if instead of ternary operator
+ // after bumping requirements to C++14
+ return (r == R) ? E0 : next.extent(r);
+ }
+ /*! \brief Report the static extent of dimension r.
+ * \param[in] r the dimension to query
+ * \returns the static extent in dimension r.
+ */
+ static constexpr std::ptrdiff_t static_extent(const std::size_t r) noexcept
+ {
+ // TODO use early return and if instead of ternary operator
+ // after bumping requirements to C++14
+ return (r == R) ? E0 : next_extents_analyse::static_extent(r);
+ }
+};
+
+/*! \libinternal \brief Enable querying extent of specific rank by splitting
+ * a static extent off the variadic template arguments.
+ */
+template< int R, std::ptrdiff_t ... StaticExtents >
+struct extents_analyse<R, dynamic_extent, StaticExtents...> {
+ //! The extent analysis of the next lower rank.
+ using next_extents_analyse = extents_analyse<R-1, StaticExtents...>;
+ /*! \brief Accumulate the total rank from all extents.
+ * \returns incremented rank of the next extent
+ */
+ static constexpr std::size_t rank() noexcept { return next_extents_analyse::rank()+1; }
+ /*! \brief Accumulate the dynamic rank from all extents.
+ * \returns the dynamic rank of the next extent analysis.
+ */
+ static constexpr std::size_t rank_dynamic() noexcept { return next_extents_analyse::rank_dynamic()+1; }
+
+ //! Store analysis of the next extent of next lower rank.
+ next_extents_analyse next;
+ //! The dynamic extent of this rank
+ std::ptrdiff_t this_extent;
+
+ //! Trivial constructor.
+ extents_analyse() : next(), this_extent(0) {}
+
+ /*! \brief Construction from dynamic extents hands the extents down
+ * to the next extents analysis of lower rank.
+ * \param[in] E the dynamic extent of this rank.
+ * \param[in] de dynamic extents
+ */
+ template<class ... DynamicExtents>
+ extents_analyse(std::ptrdiff_t E, DynamicExtents... de) : next(de ...), this_extent(E) {}
+
+ /*! \brief Construct from an array of dynamic extentes and rank.
+ * Hand down the dynamic rank parameters to the next extents analysis rank
+ * \param[in] de dynamic extents
+ * \param[in] r rank to read from the dynamic extent
+ */
+ template<std::size_t Rank>
+ extents_analyse(const std::array<std::ptrdiff_t, Rank> &de, const std::size_t r) : next(de, r+1), this_extent(de[r]) {}
+
+ //! Copy constructor.
+ template<std::ptrdiff_t... OtherStaticExtents>
+ extents_analyse(extents_analyse<R, OtherStaticExtents...> rhs) : next(rhs.next), this_extent(rhs.extent(R)) {}
+
+ //! Assignment operator.
+ template<std::ptrdiff_t... OtherStaticExtents>
+ extents_analyse &operator= (extents_analyse<R, OtherStaticExtents...> rhs)
+ {
+ next = rhs.next;
+ this_extent = rhs.extent(R);
+ return *this;
+ }
+
+ /*! \brief Report extent of dimension r.
+ * \param[in] r the dimension to query
+ * \returns the extent in dimension r.
+ */
+ constexpr std::ptrdiff_t extent(const std::size_t r) const noexcept
+ {
+ return (r == R) ? this_extent : next.extent(r); // TODO use early return and if instead of ternary operator after bumping requirements to C++14
+ }
+ /*! \brief Report the static extent of dimension r.
+ * \param[in] r the dimension to query
+ * \returns the static extent in dimension r.
+ */
+ static constexpr std::ptrdiff_t static_extent(const std::size_t r) noexcept
+ {
+ return (r == R) ? dynamic_extent : next_extents_analyse::static_extent(r); // TODO use early return and if instead of ternary operator after bumping requirements to C++14
+ }
+};
+
+/*! \libinternal \brief Specialisation for rank 0 extents analysis.
+ * Ends recursive rank analysis.
+ */
+template<>
+struct extents_analyse<0> {
+ /*! \brief Rank of extent of rank 0.
+ * \returns 0
+ */
+ static constexpr std::size_t rank() noexcept { return 0; }
+ /*! \brief Dynamic rank of extent of rank 0.
+ * \returns 0
+ */
+ static constexpr std::size_t rank_dynamic() noexcept { return 0; }
+
+ //! Trivial constructor.
+ extents_analyse() {}
+
+ //! Construct from array and rank, doing nothing.
+ template<std::size_t Rank>
+ extents_analyse(const std::array<std::ptrdiff_t, Rank> & /*de*/, const std::size_t /*r*/) {}
+
+ //extents_analyse & operator=(extents_analyse) = default;
+
+ /*! \brief Extent of rank 0 is 1, ensuring that product of extents yields required size and not zero.
+ * NOTE changed from ORNL reference implementation in making this static constexpr instead of constexpr .. const
+ */
+ static constexpr std::ptrdiff_t extent(const std::size_t /*r*/) noexcept
+ {
+ return 1;
+ }
+
+ //! Static extent of rank 0 is 1, ensuring that product of extents yields required size and not zero.
+ static constexpr std::ptrdiff_t static_extent(const std::size_t /*r*/) noexcept
+ {
+ return 1;
+ }
+
+};
+} // namespace detail
+
+
+/*! \libinternal \brief Multidimensional extents with static and dynamic dimensions.
+ *
+ * Describes a multidimensional index space of rank R.
+ * This is equivalent to the Cartesian product space of integer intervals
+ * [0, N_0) x [0, N_1) x ... x [0,N_{R-1} )
+ *
+ * Confer to P0009r8 of the Library Evolution Working Group and mdspan.extents
+ *
+ * \tparam StaticExtents rank number of extents, where the dynamic_extent
+ * constant for static extent is used to signal a dynamic extent.
+ */
+template< std::ptrdiff_t ... StaticExtents >
+class extents
+{
+ private:
+ using extents_analyse_t = detail::extents_analyse<sizeof ... (StaticExtents), StaticExtents...>;
+
+ public:
+ //! Type used to index elements.
+ using index_type = std::ptrdiff_t;
+ //! Trivial constructor
+ constexpr extents() noexcept {}
+ //! Move constructor
+ constexpr extents( extents && ) noexcept = default;
+ //! Copy constructor.
+ constexpr extents( const extents & ) noexcept = default;
+ /*! \brief Construct with dynamic extents.
+ *
+ * Allows for extents(u,v,w..) syntax when setting dynamic extents
+ *
+ * \tparam IndexType type of index
+ * \param[in] dn first dynamic index
+ * \param[in] DynamicExtents parameter pack
+ */
+ template< class ... IndexType >
+ constexpr extents( std::ptrdiff_t dn,
+ IndexType ... DynamicExtents ) noexcept
+ : impl( dn, DynamicExtents ... )
+ { static_assert( 1+sizeof ... (DynamicExtents) == rank_dynamic(), "" ); }
+
+ /*! \brief Construct from array of dynamic extents.
+ *
+ * Allows for extents({{u,v,w..}}) syntax when setting dynamic extents
+ *
+ * \param[in] dynamic_extents array of dynamic rank size containing extents
+ */
+ constexpr extents( const std::array<std::ptrdiff_t, extents_analyse_t::rank_dynamic()> dynamic_extents) noexcept
+ : impl(dynamic_extents, 0) {}
+
+ //! Copy constructor
+ template<std::ptrdiff_t... OtherStaticExtents>
+ extents( const extents<OtherStaticExtents...> &other )
+ : impl( other.impl ) {}
+
+ //! Default move assignment
+ extents &operator= ( extents && ) noexcept = default;
+ //! Default copy assignment
+ extents &operator= ( const extents & ) noexcept = default;
+ //! Copy assignment
+ template<std::ptrdiff_t... OtherStaticExtents>
+ extents &operator= ( const extents<OtherStaticExtents...> &other )
+ { impl = other.impl; return *this; }
+ //! Default destructor
+ ~extents() = default;
+
+ // [mdspan.extents.obs]
+ /*! \brief The rank of the extent.
+ * \returns the rank all extents together
+ */
+ static constexpr std::size_t rank() noexcept
+ { return sizeof ... (StaticExtents); }
+ /*! \brief The rank of the dynamic extents.
+ * \returns Only the dynamic extents.
+ */
+ static constexpr std::size_t rank_dynamic() noexcept
+ { return extents_analyse_t::rank_dynamic(); }
+ /*! \brief The rank of the static extents.
+ * \returns Only the static extents.
+ */
+ static constexpr index_type static_extent(std::size_t k) noexcept
+ { return extents_analyse_t::static_extent(rank()-k); }
+ /*! \brief The extent along a specific dimension.
+ * \param[in] k the dimension
+ * \returns the extent along that dimension
+ */
+ constexpr index_type extent(std::size_t k) const noexcept
+ { return impl.extent(rank()-k); }
+ private:
+ //! For copy assignment, extents are friends of extents.
+ template< std::ptrdiff_t... > friend class extents;
+ //! The implementation class.
+ extents_analyse_t impl;
+};
+
+
+/*! \brief Comparison operator.
+ * \returns true if extents are equal
+ * TODO add constexpr when C++14 is required
+ */
+template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
+bool operator==(const extents<LHS...> &lhs,
+ const extents<RHS...> &rhs) noexcept
+{
+ bool equal = lhs.rank() == rhs.rank();
+ for (std::size_t r = 0; r < lhs.rank(); r++)
+ {
+ equal = equal && ( lhs.extent(r) == rhs.extent(r) );
+ }
+ return equal;
+}
+
+/*! \brief Check for non-equality.
+ * \returns true if extents are unequal
+ */
+template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
+constexpr bool operator!=(const extents<LHS...> &lhs,
+ const extents<RHS...> &rhs) noexcept
+{
+ return !(lhs == rhs);
+}
+
+} // namespace gmx
+#endif /* end of include guard: MDSPAN_EXTENTS_H */
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2018, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(MDSpanTests mdspan-test
+ extents.cpp
+ )
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*
+ * This file is a modified version of original work of Sandia Corporation.
+ * In the spirit of the original code, this particular file can be distributed
+ * on the terms of Sandia Corporation.
+ */
+/*
+ * Kokkos v. 2.0
+ * Copyright (2014) Sandia Corporation
+ *
+ * Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+ * the U.S. Government retains certain rights in this software.
+ *
+ * Kokkos is licensed under 3-clause BSD terms of use:
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are
+ * met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * 2. 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.
+ *
+ * 3. Neither the name of the Corporation nor the names of the
+ * contributors may be used to endorse or promote products derived from
+ * this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "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 SANDIA CORPORATION OR THE
+ * 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.
+ *
+ * Questions? Contact Christian R. Trott (crtrott@sandia.gov)
+ */
+/*! \internal \file
+ * \brief Testing gmx::extents.
+ *
+ * \author Christian Trott <crtrott@sandia.gov>
+ * \author Carter Edwards <hedwards@nvidia.com>
+ * \author David Hollman <dshollm@sandia.gov>
+ * \author Christian Blau <cblau@gwdg.de>
+ */
+#include "gmxpre.h"
+
+#include "gromacs/mdspan/extents.h"
+
+#include <gtest/gtest.h>
+
+namespace gmx
+{
+
+template<ptrdiff_t ... E_STATIC>
+class ExtentsTest
+{
+ public:
+ using extents_type = gmx::extents<E_STATIC...>;
+
+ extents_type my_extents_explicit;
+ extents_type my_extents_array;
+ extents_type my_extents_copy;
+
+ ExtentsTest()
+ {
+ my_extents_explicit = extents<E_STATIC...>();
+ my_extents_array = extents<E_STATIC...>(std::array<ptrdiff_t, 0>());
+ my_extents_copy = extents<E_STATIC...>(my_extents_explicit);
+ }
+
+ template<class ... E>
+ ExtentsTest(E ... e)
+ {
+ my_extents_explicit = extents<E_STATIC...>(e ...);
+ my_extents_array = extents<E_STATIC...>(std::array<ptrdiff_t, 2>({{e ...}}));
+ my_extents_copy = extents<E_STATIC...>(my_extents_explicit);
+ }
+
+ void check_rank(ptrdiff_t r)
+ {
+ EXPECT_EQ(my_extents_explicit.rank(), r);
+ EXPECT_EQ(my_extents_array.rank(), r);
+ EXPECT_EQ(my_extents_copy.rank(), r);
+ }
+ void check_rank_dynamic(ptrdiff_t r)
+ {
+ EXPECT_EQ(my_extents_explicit.rank_dynamic(), r);
+ EXPECT_EQ(my_extents_array.rank_dynamic(), r);
+ EXPECT_EQ(my_extents_copy.rank_dynamic(), r);
+ }
+ template<class ... E>
+ void check_extents(E ... e)
+ {
+ std::array<ptrdiff_t, extents_type::rank()> s = {{E_STATIC ...}};
+ std::array<ptrdiff_t, extents_type::rank()> a = {{e ...}};
+ for (size_t r = 0; r < extents_type::rank(); r++)
+ {
+ EXPECT_EQ(my_extents_explicit.static_extent(r), s[r]);
+ EXPECT_EQ(my_extents_explicit.extent(r), a[r]);
+
+ EXPECT_EQ(my_extents_array.static_extent(r), s[r]);
+ EXPECT_EQ(my_extents_array.extent(r), a[r]);
+
+ EXPECT_EQ(my_extents_copy.static_extent(r), s[r]);
+ EXPECT_EQ(my_extents_copy.extent(r), a[r]);
+ }
+ EXPECT_EQ(my_extents_explicit.static_extent(extents_type::rank()+1), 1);
+ EXPECT_EQ(my_extents_explicit.extent(extents_type::rank()+1), 1);
+
+ EXPECT_EQ(my_extents_array.static_extent(extents_type::rank()+1), 1);
+ EXPECT_EQ(my_extents_array.extent(extents_type::rank()+1), 1);
+
+ EXPECT_EQ(my_extents_copy.static_extent(extents_type::rank()+1), 1);
+ EXPECT_EQ(my_extents_copy.extent(extents_type::rank()+1), 1);
+ }
+
+};
+
+TEST(ExtentsTest, Construction) {
+
+ // setting two dynamic extents
+ ExtentsTest<5, dynamic_extent, 3, dynamic_extent, 1> test(4, 2);
+
+ test.check_rank(5);
+ test.check_rank_dynamic(2);
+ test.check_extents(5, 4, 3, 2, 1);
+
+}
+
+TEST(ExtentsTest, PurelyStatic) {
+ ExtentsTest<5, 4, 3> test;
+ test.check_rank(3);
+ test.check_rank_dynamic(0);
+ test.check_extents(5, 4, 3);
+}
+
+TEST(ExtentsTest, RankNought) {
+ // Can construct extents of rank nought
+ ExtentsTest<> test;
+ test.check_rank(0);
+ test.check_rank_dynamic(0);
+}
+TEST(ExtentsTest, Assignment) {
+ extents<5, dynamic_extent, 3, dynamic_extent, 1> e1(4, 2);
+ extents<5, 4, 3, 2, 1> e2;
+ e2 = e1;
+ for (size_t r = 0; r < 5; r++)
+ {
+ EXPECT_EQ(e2.extent(r), e1.extent(r));
+ }
+ extents<dynamic_extent, dynamic_extent, dynamic_extent, dynamic_extent, dynamic_extent> e3(9, 8, 7, 6, 5);
+ for (int r = 0; r < 5; r++)
+ {
+ EXPECT_EQ(e3.extent(r), 9-r);
+ }
+ e3 = e1;
+ for (int r = 0; r < 5; r++)
+ {
+ EXPECT_EQ(e3.extent(r), e1.extent(r));
+ }
+}
+} // namespace gmx
*/
static void MCL_init_client(const char *) // NOLINT(readability-named-parameter)
{
- gmx_fatal(FARGS, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
+ GMX_RELEASE_ASSERT(GMX_MIMIC, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
}
/*! \brief Stub communication library function to call in case if
*/
static void MCL_send(void *, int, int, int) // NOLINT(readability-named-parameter)
{
- gmx_fatal(FARGS, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
+ GMX_RELEASE_ASSERT(GMX_MIMIC, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
}
/*! \brief Stub communication library function to call in case if
*/
static void MCL_receive(void *, int, int, int) // NOLINT(readability-named-parameter)
{
- gmx_fatal(FARGS, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
+ GMX_RELEASE_ASSERT(GMX_MIMIC, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
}
/*! \brief Stub communication library function to call in case if
* GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
*/
-static void MCL_destroy() // NOLINT(readability-named-parameter)
+static void MCL_destroy()
{
- gmx_fatal(FARGS, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
+ GMX_RELEASE_ASSERT(GMX_MIMIC, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
}
#endif
/* In parallel, store we need to extract localWeights from weights at DD time */
std::vector<real> &weights = ((cr && PAR(cr)) ? pg->globalWeights : pg->localWeights);
- const gmx_groups_t *groups = &mtop->groups;
+ const gmx_groups_t &groups = mtop->groups;
/* Count frozen dimensions and (weighted) mass */
int nfrozen = 0;
}
else
{
- if (groups->grpnr[egcTC] == nullptr)
+ if (groups.grpnr[egcTC] == nullptr)
{
mbd = ir->delta_t/ir->opts.tau_t[0];
}
else
{
- mbd = ir->delta_t/ir->opts.tau_t[groups->grpnr[egcTC][ii]];
+ mbd = ir->delta_t/ir->opts.tau_t[groups.grpnr[egcTC][ii]];
}
}
w *= m/mbd;
top[0] = gmx_mtop_t_to_t_topology(&mtop[0], false);
top[1] = gmx_mtop_t_to_t_topology(&mtop[1], false);
cmp_top(stdout, &top[0], &top[1], ftol, abstol);
- cmp_groups(stdout, &mtop[0].groups, &mtop[1].groups,
- mtop[0].natoms, mtop[1].natoms);
+ compareAtomGroups(stdout, mtop[0].groups, mtop[1].groups,
+ mtop[0].natoms, mtop[1].natoms);
comp_state(&state[0], &state[1], bRMSD, ftol, abstol);
}
else
t_state state;
t_tpxheader tpx;
gmx_mtop_t mtop;
- gmx_groups_t *groups;
t_topology top;
read_tpxheader(fn, &tpx, TRUE);
pr_rvecs(stdout, indent, "v", tpx.bV ? state.v.rvec_array() : nullptr, state.natoms);
}
- groups = &mtop.groups;
+ const gmx_groups_t &groups = mtop.groups;
snew(gcount, egcNR);
for (i = 0; (i < egcNR); i++)
{
- snew(gcount[i], groups->grps[i].nr);
+ snew(gcount[i], groups.grps[i].nr);
}
for (i = 0; (i < mtop.natoms); i++)
{
atot = 0;
printf("%-12s: ", gtypes[i]);
- for (j = 0; (j < groups->grps[i].nr); j++)
+ for (j = 0; (j < groups.grps[i].nr); j++)
{
printf(" %5d", gcount[i][j]);
atot += gcount[i][j];
}
}
-void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
- int natoms0, int natoms1)
+void compareAtomGroups(FILE *fp, const gmx_groups_t &g0, const gmx_groups_t &g1,
+ int natoms0, int natoms1)
{
- char buf[32];
-
fprintf(fp, "comparing groups\n");
for (int i = 0; i < egcNR; i++)
{
- sprintf(buf, "grps[%d].nr", i);
- cmp_int(fp, buf, -1, g0->grps[i].nr, g1->grps[i].nr);
- if (g0->grps[i].nr == g1->grps[i].nr)
+ std::string buf = gmx::formatString("grps[%d].nr", i);
+ cmp_int(fp, buf.c_str(), -1, g0.grps[i].nr, g1.grps[i].nr);
+ if (g0.grps[i].nr == g1.grps[i].nr)
{
- for (int j = 0; j < g0->grps[i].nr; j++)
+ for (int j = 0; j < g0.grps[i].nr; j++)
{
- sprintf(buf, "grps[%d].name[%d]", i, j);
- cmp_str(fp, buf, -1,
- *g0->grpname[g0->grps[i].nm_ind[j]],
- *g1->grpname[g1->grps[i].nm_ind[j]]);
+ buf = gmx::formatString("grps[%d].name[%d]", i, j);
+ cmp_str(fp, buf.c_str(), -1,
+ *g0.grpname[g0.grps[i].nm_ind[j]],
+ *g1.grpname[g1.grps[i].nm_ind[j]]);
}
}
- cmp_int(fp, "ngrpnr", i, g0->ngrpnr[i], g1->ngrpnr[i]);
- if (g0->ngrpnr[i] == g1->ngrpnr[i] && natoms0 == natoms1 &&
- (g0->grpnr[i] != nullptr || g1->grpnr[i] != nullptr))
+ cmp_int(fp, "ngrpnr", i, g0.ngrpnr[i], g1.ngrpnr[i]);
+ if (g0.ngrpnr[i] == g1.ngrpnr[i] && natoms0 == natoms1 &&
+ (g0.grpnr[i] != nullptr || g1.grpnr[i] != nullptr))
{
for (int j = 0; j < natoms0; j++)
{
*/
}
-int getGroupType(const gmx_groups_t *group, int type, int atom)
+int getGroupType(const gmx_groups_t &group, int type, int atom)
{
- return (group->grpnr[type] ? group->grpnr[type][atom] : 0);
+ return (group.grpnr[type] ? group.grpnr[type][atom] : 0);
}
void copy_moltype(const gmx_moltype_t *src, gmx_moltype_t *dst)
* \param[in] type Type of group to check.
* \param[in] atom Atom to check if it has an entry.
*/
-int getGroupType (const gmx_groups_t *group, int type, int atom);
+int getGroupType (const gmx_groups_t &group, int type, int atom);
/* The global, complete system topology struct, based on molecule types.
* This structure should contain no data that is O(natoms) in memory.
gmx_bool bShowNumbers, gmx_bool bShowParameters);
void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol);
-void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
- int natoms0, int natoms1);
+
+/*! \brief Compare groups.
+ *
+ * \param[in] fp File pointer to write to.
+ * \param[in] g0 First group for comparison.
+ * \param[in] g1 Second group for comparison.
+ * \param[in] natoms0 Number of atoms for first group.
+ * \param[in] natoms1 Number of atoms for second group.
+ */
+void compareAtomGroups(FILE *fp, const gmx_groups_t &g0, const gmx_groups_t &g1,
+ int natoms0, int natoms1);
//! Deleter for gmx_localtop_t, needed until it has a proper destructor.
using ExpandedTopologyPtr = gmx::unique_cptr<gmx_localtop_t, done_and_sfree_localtop>;
{ "Why would the backup server database get corrupted anyway?", "Stefan Fleischmann -- system administrator, physicist, optimist." },
{ "Teaching quantum computing is like teaching computer science at Hogwarts.", "Thomas Sterling, ISC2018 keynote" },
{ "It is unfortunate that the authors did not make better use of all the electric power energy that went into these massive computations.", "An anonymous referee" },
+ { "Doctor, doctor, it hurts when I hit myself in the head with the hammer! - So don't do it!", "Bjarne Stroustrup at CppCon2015" },
{ "This is extremely unlikely.", "Berk Hess" },
{ "Nothing is more anarchic than power.", "Pier Paolo Pasolini" },
};
"Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water",
"J. Chem. Phys.",
116, 2002, "9602-9610" },
- { "Hetenyi2002b",
- "Csaba Hetenyi and David van der Spoel",
- "Efficient docking of peptides to proteins without prior knowledge of the binding site.",
- "Prot. Sci.",
- 11, 2002, "1729-1737" },
{ "Hess2003",
"B. Hess and R.M. Scheek",
"Orientation restraints in molecular dynamics simulations using time and ensemble averaging",
registerModule(manager, &gmx_xpm2ps, "xpm2ps",
"Convert XPM (XPixelMap) matrices to postscript or XPM");
- registerModule(manager, &gmx_anadock, "anadock",
- "Cluster structures from Autodock runs");
registerModule(manager, &gmx_anaeig, "anaeig",
"Analyze eigenvectors/normal modes");
registerModule(manager, &gmx_analyze, "analyze",
"Analyze density of states and properties based on that");
registerModule(manager, &gmx_dyecoupl, "dyecoupl",
"Extract dye dynamics from trajectories");
- registerModule(manager, &gmx_dyndom, "dyndom",
- "Interpolate and extrapolate structure rotations");
registerModule(manager, &gmx_enemat, "enemat",
"Extract an energy matrix from an energy file");
registerModule(manager, &gmx_energy, "energy",
"Calculate residue contact maps");
registerModule(manager, &gmx_mindist, "mindist",
"Calculate the minimum distance between two groups");
- registerModule(manager, &gmx_morph, "morph",
- "Interpolate linearly between conformations");
registerModule(manager, &gmx_msd, "msd",
"Calculates mean square displacements");
registerModule(manager, &gmx_nmeig, "nmeig",
manager->addModuleGroup("Tools");
group.addModule("analyze");
group.addModule("awh");
- group.addModule("dyndom");
group.addModule("filter");
group.addModule("lie");
- group.addModule("morph");
group.addModule("pme_error");
group.addModule("sham");
group.addModule("spatial");
{
gmx::CommandLineModuleGroup group =
manager->addModuleGroup("Structural properties");
- group.addModule("anadock");
group.addModule("bundle");
group.addModule("clustsize");
group.addModule("disre");
${exename}
# files with code for tests
minimize.cpp
+ normalmodes.cpp
rerun.cpp
# pseudo-library for code for testing mdrun
$<TARGET_OBJECTS:mdrun_test_objlib>
#include <cstdio>
+#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxpreprocess/grompp.h"
#include "gromacs/hardware/detecthardware.h"
#include "gromacs/options/basicoptions.h"
tprFileName_(fileManager->getTemporaryFilePath(".tpr")),
logFileName_(fileManager->getTemporaryFilePath(".log")),
edrFileName_(fileManager->getTemporaryFilePath(".edr")),
+ mtxFileName_(fileManager->getTemporaryFilePath(".mtx")),
nsteps_(-2),
fileManager_(*fileManager)
{
gmx::TextWriter::writeFileFromString(ndxFileName_, ndxString);
}
+void
+SimulationRunner::useTopG96AndNdxFromDatabase(const std::string &name)
+{
+ topFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".top");
+ groFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".g96");
+ ndxFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".ndx");
+}
+
void
SimulationRunner::useTopGroAndNdxFromDatabase(const std::string &name)
{
return callGrompp(CommandLine());
}
+int
+SimulationRunner::callNmeig()
+{
+ /* Conforming to style guide by not passing a non-const reference
+ to this function. Passing a non-const reference might make it
+ easier to write code that incorrectly re-uses callerRef after
+ the call to this function. */
+
+ CommandLine caller;
+ caller.append("nmeig");
+ caller.addOption("-s", tprFileName_);
+ caller.addOption("-f", mtxFileName_);
+ // Ignore the overall translation and rotation in the
+ // first six eigenvectors.
+ caller.addOption("-first", "7");
+ // No need to check more than a number of output values.
+ caller.addOption("-last", "50");
+ caller.addOption("-xvg", "none");
+
+ return gmx_nmeig(caller.argc(), caller.argv());
+}
+
int
SimulationRunner::callMdrun(const CommandLine &callerRef)
{
caller.addOption("-g", logFileName_);
caller.addOption("-e", edrFileName_);
+ caller.addOption("-mtx", mtxFileName_);
caller.addOption("-o", fullPrecisionTrajectoryFileName_);
caller.addOption("-x", reducedPrecisionTrajectoryFileName_);
void useStringAsMdpFile(const std::string &mdpString);
//! Use a string as -n input to grompp
void useStringAsNdxFile(const char *ndxString);
+ //! Use a standard .top and .g96 file as input to grompp
+ void useTopG96AndNdxFromDatabase(const std::string &name);
//! Use a standard .top and .gro file as input to grompp
void useTopGroAndNdxFromDatabase(const std::string &name);
//! Use a standard .gro file as input to grompp
int callGromppOnThisRank(const CommandLine &callerRef);
//! Convenience wrapper for a default call to \c callGromppOnThisRank
int callGromppOnThisRank();
+ //! Calls nmeig for testing
+ int callNmeig();
//! Calls mdrun for testing with a customized command line
int callMdrun(const CommandLine &callerRef);
/*! \brief Convenience wrapper for calling mdrun for testing
std::string tprFileName_;
std::string logFileName_;
std::string edrFileName_;
+ std::string mtxFileName_;
std::string cptFileName_;
std::string swapFileName_;
int nsteps_;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Tests for the normal modes functionality.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include <map>
+#include <memory>
+#include <string>
+#include <tuple>
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/compat/make_unique.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/trajectory/energyframe.h"
+#include "gromacs/trajectory/trajectoryframe.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/filestream.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/mpitest.h"
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/xvgtest.h"
+
+#include "energycomparison.h"
+#include "energyreader.h"
+#include "moduletest.h"
+#include "simulationdatabase.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+//! Helper type
+using MdpField = MdpFieldValues::value_type;
+
+/*! \brief Test fixture base for normal mode analysis
+ *
+ * This test ensures mdrun can run a normal mode analys, reaching
+ * a reproducible eigenvalues following diagonalization.
+ *
+ * The choices for tolerance are arbitrary but sufficient. */
+class NormalModesTest : public MdrunTestFixture,
+ public ::testing::WithParamInterface <
+ std::tuple < std::string, std::string>>
+{
+};
+
+TEST_P(NormalModesTest, WithinTolerances)
+{
+ auto params = GetParam();
+ auto simulationName = std::get<0>(params);
+ auto integrator = std::get<1>(params);
+ SCOPED_TRACE(formatString("Comparing normal modes for '%s'",
+ simulationName.c_str()));
+
+ // TODO At some point we should also test PME-only ranks.
+ int numRanksAvailable = getNumberOfTestMpiRanks();
+ if (!isNumberOfPpRanksSupported(simulationName, numRanksAvailable))
+ {
+ fprintf(stdout, "Test system '%s' cannot run with %d ranks.\n"
+ "The supported numbers are: %s\n",
+ simulationName.c_str(), numRanksAvailable,
+ reportNumbersOfPpRanksSupported(simulationName).c_str());
+ return;
+ }
+ auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(),
+ integrator.c_str(),
+ "no", "no");
+ mdpFieldValues["nsteps"] = "1";
+ mdpFieldValues["rcoulomb"] = "5.6";
+ mdpFieldValues["rlist"] = "5.6";
+ mdpFieldValues["rvdw"] = "5.6";
+ mdpFieldValues["constraints"] = "none";
+ mdpFieldValues.insert(MdpField("coulombtype", "Cut-off"));
+ mdpFieldValues.insert(MdpField("vdwtype", "Cut-off"));
+
+ // prepare the .tpr file
+ {
+ CommandLine caller;
+ caller.append("grompp");
+ runner_.useTopG96AndNdxFromDatabase(simulationName);
+ runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
+ EXPECT_EQ(0, runner_.callGrompp(caller));
+ }
+ // Do mdrun, preparing to check the normal modes later
+ {
+ CommandLine mdrunCaller;
+ mdrunCaller.append("mdrun");
+ ASSERT_EQ(0, runner_.callMdrun(mdrunCaller));
+ }
+ // Now run gmx nmeig and check the output
+ {
+ ASSERT_EQ(0, runner_.callNmeig());
+ TestReferenceData refData;
+ auto checker = refData.rootChecker()
+ .checkCompound("System", simulationName)
+ .checkCompound("Integrator", integrator);
+ auto settings = XvgMatchSettings();
+ TextInputFile input("eigenval.xvg");
+ checkXvgFile(&input, &checker, settings);
+ }
+}
+
+//! Containers of systems and integrators to test.
+//! \{
+std::vector<std::string> systemsToTest_g = { "scaled-water" };
+std::vector<std::string> integratorsToTest_g = { "nm" };
+
+//! \}
+
+// The time for OpenCL kernel compilation means these tests might time
+// out. If that proves to be a problem, these can be disabled for
+// OpenCL builds. However, once that compilation is cached for the
+// lifetime of the whole test binary process, these tests should run in
+// such configurations.
+#if GMX_DOUBLE
+INSTANTIATE_TEST_CASE_P(NormalModesWorks, NormalModesTest,
+ ::testing::Combine(::testing::ValuesIn(systemsToTest_g),
+ ::testing::ValuesIn(integratorsToTest_g)));
+#endif
+} // namespace
+} // namespace test
+} // namespace gmx
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <System Name="scaled-water">
+ <Integrator Name="nm">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>7</Real>
+ <Real>0.068698</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>8</Real>
+ <Real>0.311942</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">2</Int>
+ <Real>9</Real>
+ <Real>0.318822</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">2</Int>
+ <Real>10</Real>
+ <Real>0.916834</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">2</Int>
+ <Real>11</Real>
+ <Real>3.24034</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">2</Int>
+ <Real>12</Real>
+ <Real>13.6069</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">2</Int>
+ <Real>13</Real>
+ <Real>14.2014</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">2</Int>
+ <Real>14</Real>
+ <Real>39.3613</Real>
+ </Sequence>
+ <Sequence Name="Row8">
+ <Int Name="Length">2</Int>
+ <Real>15</Real>
+ <Real>5257.53</Real>
+ </Sequence>
+ <Sequence Name="Row9">
+ <Int Name="Length">2</Int>
+ <Real>16</Real>
+ <Real>5280.78</Real>
+ </Sequence>
+ <Sequence Name="Row10">
+ <Int Name="Length">2</Int>
+ <Real>17</Real>
+ <Real>5315.76</Real>
+ </Sequence>
+ <Sequence Name="Row11">
+ <Int Name="Length">2</Int>
+ <Real>18</Real>
+ <Real>5340.06</Real>
+ </Sequence>
+ </XvgData>
+ </Integrator>
+ </System>
+</ReferenceData>
1, 2, 3, 4, 5, 6, 7, 8, 9
} }
},
+ // Scaled water for NMA
+ {
+ "scaled-water", { { },
+ {
+ 1, 2, 3, 4, 5, 6
+ } }
+ },
// Nonanol molecule in vacuo, topology suitable for testing FEP
// on KE, angles, dihedral restraints, coulomb and vdw
{
mdpFieldValues.insert(MdpField("compressibility", "5e-5"));
mdpFieldValues.insert(MdpField("constraints", "none"));
mdpFieldValues.insert(MdpField("other", ""));
+ mdpFieldValues.insert(MdpField("rcoulomb", "0.7"));
+ mdpFieldValues.insert(MdpField("rvdw", "0.7"));
return mdpFieldValues;
}
* energies were not computed with those from rerun on the same
* coordinates.
*/
- return formatString(R"(rcoulomb = 0.7
- rvdw = 0.7
+ return formatString(R"(rcoulomb = %s
+ rvdw = %s
rlist = -1
bd-fric = 1000
verlet-buffer-tolerance = 0.000001
lincs-order = 2
lincs-iter = 5
%s)",
+ mdpFieldValues.at("rcoulomb").c_str(),
+ mdpFieldValues.at("rvdw").c_str(),
mdpFieldValues.at("nsteps").c_str(),
mdpFieldValues.at("integrator").c_str(),
mdpFieldValues.at("tcoupl").c_str(),
#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/commandline/cmdlineprogramcontext.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringstream.h"
setInputFile(option, filename.c_str());
}
+void CommandLineTestBase::setModifiableInputFile(
+ const char *option, const std::string &filename)
+{
+ setModifiableInputFile(option, filename.c_str());
+}
+
+void CommandLineTestBase::setModifiableInputFile(
+ const char *option, const char *filename)
+{
+ std::string originalFileName = gmx::test::TestFileManager::getInputFilePath(filename);
+ std::string modifiableFileName = fileManager().getTemporaryFilePath(filename);
+ gmx_file_copy(originalFileName.c_str(), modifiableFileName.c_str(), true);
+ impl_->cmdline_.addOption(option, modifiableFileName);
+}
+
void CommandLineTestBase::setInputFileContents(
const char *option, const char *extension, const std::string &contents)
{
impl_->helper_.setOutputFile(&impl_->cmdline_, option, filename, matcher);
}
+void CommandLineTestBase::setInputAndOutputFile(
+ const char *option, const char *filename,
+ const ITextBlockMatcherSettings &matcher)
+{
+ std::string originalFileName = gmx::test::TestFileManager::getInputFilePath(filename);
+ std::string modifiableFileName = fileManager().getTemporaryFilePath(filename);
+ gmx_file_copy(originalFileName.c_str(), modifiableFileName.c_str(), true);
+ impl_->helper_.setOutputFile(&impl_->cmdline_, option, filename, matcher);
+}
+
+void CommandLineTestBase::setInputAndOutputFile(
+ const char *option, const char *filename,
+ const IFileMatcherSettings &matcher)
+{
+ std::string originalFileName = gmx::test::TestFileManager::getInputFilePath(filename);
+ std::string modifiableFileName = fileManager().getTemporaryFilePath(filename);
+ gmx_file_copy(originalFileName.c_str(), modifiableFileName.c_str(), true);
+ impl_->helper_.setOutputFile(&impl_->cmdline_, option, filename, matcher);
+}
+
CommandLine &CommandLineTestBase::commandLine()
{
return impl_->cmdline_;
void setInputFile(const char *option, const char *filename);
//! \copydoc setInputFile(const char *, const char *);
void setInputFile(const char *option, const std::string &filename);
+ /*! \brief
+ * Sets an input file that may be modified. The file is copied to a
+ * temporary file, which is used as the test input
+ *
+ * \param[in] option Option to set.
+ * \param[in] filename Name of the input file.
+ *
+ */
+ void setModifiableInputFile(const char *option, const char *filename);
+ //! \copydoc setModifiableInputFile(const char *, const char *);
+ void setModifiableInputFile(const char *option, const std::string &filename);
/*! \brief
* Generates and sets an input file.
*
*/
void setOutputFile(const char *option, const char *filename,
const IFileMatcherSettings &matcher);
+ /*! \brief
+ * Sets a file parameter that is used for input and modified as output. The input file
+ * is copied to a temporary file that is used as input and can be modified.
+ */
+ void setInputAndOutputFile(const char *option, const char *filename,
+ const ITextBlockMatcherSettings &matcher);
+ //! \copydoc setInputAndOutputFile(const char *, const char *, const ITextBlockMatcherSettings&);
+ void setInputAndOutputFile(const char *option, const char *filename,
+ const IFileMatcherSettings &matcher);
/*! \brief
* Returns the internal CommandLine object used to construct the
--- /dev/null
+TITLE
+2 scaled waters
+END
+POSITION
+ 1 SOL OW 1 0.914818904 17.114674936 24.974532564
+ 1 SOL HW1 2 1.207239659 16.434171182 24.367718701
+ 1 SOL HW2 3 1.794362088 17.256320895 0.323592571
+ 2 SOL OW 4 2.688663748 14.887261002 23.182636745
+ 2 SOL HW1 5 2.999853477 14.939893657 22.278872288
+ 2 SOL HW2 6 2.760097525 13.938314213 23.286543655
+END
+BOX
+ 25.001000000 25.001000000 25.001000000
+END
--- /dev/null
+[ System ]
+ 1 2 3 4 5 6
+[ Water ]
+ 1 2 3 4 5 6
+[ SOL ]
+ 1 2 3 4 5 6
--- /dev/null
+[ defaults ]
+; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
+1 3 yes 0.5 0.5
+
+[ atomtypes ]
+; full atom descriptions are available in ffoplsaa.atp
+; name bond_type mass charge ptype sigma epsilon
+ OW O 8 15.99940 0.000 A 3 50
+ HW H 1 1.00800 0.000 A 0.00000e+00 0.00000e+00
+
+[ moleculetype ]
+; molname nrexcl
+SOL 2
+
+[ atoms ]
+; id at type res nr residu name at name cg nr charge
+1 OW 1 SOL OW 1 -0.6
+2 HW 1 SOL HW1 1 0.3
+3 HW 1 SOL HW2 1 0.3
+
+[ bonds ]
+; i j funct length force.c.
+1 2 1 0.9572 5024.0
+1 3 1 0.9572 5024.0
+
+[ angles ]
+; i j k funct angle force.c.
+2 1 3 1 100.0 6.0
+
+[ system ]
+2 scaled waters
+
+[ molecules ]
+SOL 2
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff