atomprop.h
atoms.h
block.h
+ forcefieldparameters.h
idef.h
ifunc.h
index.h
--- /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) 2013,2014,2015,2016,2018, 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 "forcefieldparameters.h"
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/txtdump.h"
+
+static void pr_cmap(FILE *fp, int indent, const char *title,
+ const gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
+{
+ int i, j, nelem;
+ real dx, idx;
+
+ dx = 360.0 / cmap_grid->grid_spacing;
+ nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
+
+ if (available(fp, cmap_grid, indent, title))
+ {
+ fprintf(fp, "%s\n", title);
+
+ for (i = 0; i < static_cast<int>(cmap_grid->cmapdata.size()); i++)
+ {
+ idx = -180.0;
+ fprintf(fp, "%8s %8s %8s %8s\n", "V", "dVdx", "dVdy", "d2dV");
+
+ fprintf(fp, "grid[%3d]={\n", bShowNumbers ? i : -1);
+
+ for (j = 0; j < nelem; j++)
+ {
+ if ( (j%cmap_grid->grid_spacing) == 0)
+ {
+ fprintf(fp, "%8.1f\n", idx);
+ idx += dx;
+ }
+
+ fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4]);
+ fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+1]);
+ fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+2]);
+ fprintf(fp, "%8.3f\n", cmap_grid->cmapdata[i].cmap[j*4+3]);
+ }
+ fprintf(fp, "\n");
+ }
+ }
+
+}
+
+void pr_ffparams(FILE *fp, int indent, const char *title,
+ const gmx_ffparams_t *ffparams,
+ gmx_bool bShowNumbers)
+{
+ int i;
+
+ indent = pr_title(fp, indent, title);
+ pr_indent(fp, indent);
+ fprintf(fp, "atnr=%d\n", ffparams->atnr);
+ pr_indent(fp, indent);
+ fprintf(fp, "ntypes=%d\n", ffparams->numTypes());
+ for (i = 0; i < ffparams->numTypes(); i++)
+ {
+ pr_indent(fp, indent+INDENT);
+ fprintf(fp, "functype[%d]=%s, ",
+ bShowNumbers ? i : -1,
+ interaction_function[ffparams->functype[i]].name);
+ pr_iparams(fp, ffparams->functype[i], &ffparams->iparams[i]);
+ }
+ pr_double(fp, indent, "reppow", ffparams->reppow);
+ pr_real(fp, indent, "fudgeQQ", ffparams->fudgeQQ);
+ pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers);
+}
--- /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) 2013,2014,2015,2016,2018, 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.
+ */
+#ifndef GMX_TOPOLOGY_FORCEFIELDPARAMETERS_H
+#define GMX_TOPOLOGY_FORCEFIELDPARAMETERS_H
+
+#include <cstdio>
+
+#include <vector>
+
+#include "gromacs/topology/idef.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
+
+/*! \brief Struct that holds all force field parameters for the simulated system */
+struct gmx_ffparams_t
+{
+ /*! \brief Returns the number of function types, which matches the number of elements in iparams */
+ int numTypes() const
+ {
+ GMX_ASSERT(iparams.size() == functype.size(), "Parameters and function types go together");
+
+ return functype.size();
+ }
+
+ /* TODO: Consider merging functype and iparams, either by storing
+ * the functype in t_iparams or by putting both in a single class.
+ */
+ int atnr = 0; /**< The number of non-bonded atom types */
+ std::vector<t_functype> functype; /**< The function type per type */
+ std::vector<t_iparams> iparams; /**< Force field parameters per type */
+ double reppow = 0; /**< The repulsion power for VdW: C12*r^-reppow */
+ real fudgeQQ = 0; /**< The scaling factor for Coulomb 1-4: f*q1*q2 */
+ gmx_cmap_t cmap_grid; /**< The dihedral correction maps */
+};
+
+void pr_ffparams(FILE *fp, int indent, const char *title,
+ const gmx_ffparams_t *ffparams, gmx_bool bShowNumbers);
+
+#endif
bShowNumbers, bShowParameters, iparams);
}
-static void pr_cmap(FILE *fp, int indent, const char *title,
- const gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
-{
- int i, j, nelem;
- real dx, idx;
-
- dx = 360.0 / cmap_grid->grid_spacing;
- nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
-
- if (available(fp, cmap_grid, indent, title))
- {
- fprintf(fp, "%s\n", title);
-
- for (i = 0; i < static_cast<int>(cmap_grid->cmapdata.size()); i++)
- {
- idx = -180.0;
- fprintf(fp, "%8s %8s %8s %8s\n", "V", "dVdx", "dVdy", "d2dV");
-
- fprintf(fp, "grid[%3d]={\n", bShowNumbers ? i : -1);
-
- for (j = 0; j < nelem; j++)
- {
- if ( (j%cmap_grid->grid_spacing) == 0)
- {
- fprintf(fp, "%8.1f\n", idx);
- idx += dx;
- }
-
- fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4]);
- fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+1]);
- fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+2]);
- fprintf(fp, "%8.3f\n", cmap_grid->cmapdata[i].cmap[j*4+3]);
- }
- fprintf(fp, "\n");
- }
- }
-
-}
-
-void pr_ffparams(FILE *fp, int indent, const char *title,
- const gmx_ffparams_t *ffparams,
- gmx_bool bShowNumbers)
-{
- int i;
-
- indent = pr_title(fp, indent, title);
- pr_indent(fp, indent);
- fprintf(fp, "atnr=%d\n", ffparams->atnr);
- pr_indent(fp, indent);
- fprintf(fp, "ntypes=%d\n", ffparams->numTypes());
- for (i = 0; i < ffparams->numTypes(); i++)
- {
- pr_indent(fp, indent+INDENT);
- fprintf(fp, "functype[%d]=%s, ",
- bShowNumbers ? i : -1,
- interaction_function[ffparams->functype[i]].name);
- pr_iparams(fp, ffparams->functype[i], &ffparams->iparams[i]);
- }
- pr_double(fp, indent, "reppow", ffparams->reppow);
- pr_real(fp, indent, "fudgeQQ", ffparams->fudgeQQ);
- pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers);
-}
-
void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
gmx_bool bShowNumbers, gmx_bool bShowParameters)
{
#ifndef GMX_TOPOLOGY_IDEF_H
#define GMX_TOPOLOGY_IDEF_H
-#include <stdio.h>
+#include <cstdio>
#include <array>
#include <vector>
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
typedef union t_iparams
};
-/* Struct that holds all force field parameters for the simulated system */
-struct gmx_ffparams_t
-{
- /* Returns the number of function types, which matches the number of elements in iparams */
- int numTypes() const
- {
- GMX_ASSERT(iparams.size() == functype.size(), "Parameters and function types go together");
-
- return functype.size();
- }
-
- /* TODO: Consider merging functype and iparams, either by storing
- * the functype in t_iparams or by putting both in a single class.
- */
- int atnr = 0; /* The number of non-bonded atom types */
- std::vector<t_functype> functype; /* The function type per type */
- std::vector<t_iparams> iparams; /* Force field parameters per type */
- double reppow = 0.0; /* The repulsion power for VdW: C12*r^-reppow */
- real fudgeQQ = 0._real; /* The scaling factor for Coulomb 1-4: f*q1*q2 */
- gmx_cmap_t cmap_grid; /* The dihedral correction maps */
-};
-
enum {
ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
};
const t_functype *functype, const InteractionList &ilist,
gmx_bool bShowNumbers,
gmx_bool bShowParameters, const t_iparams *iparams);
-void pr_ffparams(FILE *fp, int indent, const char *title,
- const gmx_ffparams_t *ffparams, gmx_bool bShowNumbers);
void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
gmx_bool bShowNumbers, gmx_bool bShowParameters);
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/block.h"
+#include "gromacs/topology/forcefieldparameters.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/unique_cptr.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff