-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
- *
- * If you want to redistribute modifications, 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 www.gromacs.org.
- *
+ *
+ * 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 papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#ifdef GMX_THREAD_MPI
-#include <thread_mpi.h>
-#endif
+#include "gromacs/legacyheaders/nonbonded.h"
+
+#include "config.h"
#include <stdio.h>
#include <stdlib.h>
-#include "typedefs.h"
-#include "txtdump.h"
-#include "smalloc.h"
-#include "ns.h"
-#include "vec.h"
-#include "maths.h"
-#include "macros.h"
-#include "string2.h"
-#include "force.h"
-#include "names.h"
-#include "main.h"
-#include "xvgr.h"
-#include "gmx_fatal.h"
-#include "physics.h"
-#include "force.h"
-#include "bondf.h"
-#include "nrnb.h"
-#include "smalloc.h"
-#include "nonbonded.h"
-
-#include "nb_kernel.h"
-#include "nb_free_energy.h"
-#include "nb_generic.h"
-#include "nb_generic_cg.h"
-#include "nb_generic_adress.h"
-
-/* Different default (c) and accelerated interaction-specific kernels */
-#include "nb_kernel_c/nb_kernel_c.h"
-
-#if (defined GMX_CPU_ACCELERATION_X86_SSE2) && !(defined GMX_DOUBLE)
-# include "nb_kernel_sse2_single/nb_kernel_sse2_single.h"
+
+#include "thread_mpi/threads.h"
+
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_adress.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_cg.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/simd/simd.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
+/* Different default (c) and SIMD instructions interaction-specific kernels */
+#include "gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h"
+
+#if (defined GMX_SIMD_X86_SSE2) && !(defined GMX_DOUBLE)
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h"
+#endif
+#if (defined GMX_SIMD_X86_SSE4_1) && !(defined GMX_DOUBLE)
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1) && !(defined GMX_DOUBLE)
-# include "nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
+#if (defined GMX_SIMD_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
+# include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
-# include "nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
+#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER) && !(defined GMX_DOUBLE)
+# include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_256) && !(defined GMX_DOUBLE)
-# include "nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
+#if (defined GMX_SIMD_X86_SSE2 && defined GMX_DOUBLE)
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h"
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_SSE2 && defined GMX_DOUBLE)
-# include "nb_kernel_sse2_double/nb_kernel_sse2_double.h"
+#if (defined GMX_SIMD_X86_SSE4_1 && defined GMX_DOUBLE)
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1 && defined GMX_DOUBLE)
-# include "nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
+#if (defined GMX_SIMD_X86_AVX_128_FMA && defined GMX_DOUBLE)
+# include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA && defined GMX_DOUBLE)
-# include "nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
+#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER && defined GMX_DOUBLE)
+# include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_256 && defined GMX_DOUBLE)
-# include "nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
+#if (defined GMX_SIMD_SPARC64_HPC_ACE && defined GMX_DOUBLE)
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
#endif
-#ifdef GMX_THREAD_MPI
static tMPI_Thread_mutex_t nonbonded_setup_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-#endif
static gmx_bool nonbonded_setup_done = FALSE;
void
-gmx_nonbonded_setup(FILE * fplog,
- t_forcerec * fr,
+gmx_nonbonded_setup(t_forcerec * fr,
gmx_bool bGenericKernelOnly)
{
-#ifdef GMX_THREAD_MPI
tMPI_Thread_mutex_lock(&nonbonded_setup_mutex);
-#endif
/* Here we are guaranteed only one thread made it. */
- if(nonbonded_setup_done==FALSE)
+ if (nonbonded_setup_done == FALSE)
{
- if(bGenericKernelOnly==FALSE)
+ if (bGenericKernelOnly == FALSE)
{
/* Add the generic kernels to the structure stored statically in nb_kernel.c */
- nb_kernel_list_add_kernels(kernellist_c,kernellist_c_size);
-
- if(!(fr!=NULL && fr->use_cpu_acceleration==FALSE))
+ nb_kernel_list_add_kernels(kernellist_c, kernellist_c_size);
+
+ if (!(fr != NULL && fr->use_simd_kernels == FALSE))
{
/* Add interaction-specific kernels for different architectures */
/* Single precision */
-#if (defined GMX_CPU_ACCELERATION_X86_SSE2) && !(defined GMX_DOUBLE)
- nb_kernel_list_add_kernels(kernellist_sse2_single,kernellist_sse2_single_size);
+#if (defined GMX_SIMD_X86_SSE2) && !(defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sse2_single, kernellist_sse2_single_size);
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1) && !(defined GMX_DOUBLE)
- nb_kernel_list_add_kernels(kernellist_sse4_1_single,kernellist_sse4_1_single_size);
+#if (defined GMX_SIMD_X86_SSE4_1) && !(defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sse4_1_single, kernellist_sse4_1_single_size);
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
- nb_kernel_list_add_kernels(kernellist_avx_128_fma_single,kernellist_avx_128_fma_single_size);
+#if (defined GMX_SIMD_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_avx_128_fma_single, kernellist_avx_128_fma_single_size);
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_256) && !(defined GMX_DOUBLE)
- nb_kernel_list_add_kernels(kernellist_avx_256_single,kernellist_avx_256_single_size);
+#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER) && !(defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_avx_256_single, kernellist_avx_256_single_size);
#endif
/* Double precision */
-#if (defined GMX_CPU_ACCELERATION_X86_SSE2 && defined GMX_DOUBLE)
- nb_kernel_list_add_kernels(kernellist_sse2_double,kernellist_sse2_double_size);
+#if (defined GMX_SIMD_X86_SSE2 && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sse2_double, kernellist_sse2_double_size);
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1 && defined GMX_DOUBLE)
- nb_kernel_list_add_kernels(kernellist_sse4_1_double,kernellist_sse4_1_double_size);
+#if (defined GMX_SIMD_X86_SSE4_1 && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sse4_1_double, kernellist_sse4_1_double_size);
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA && defined GMX_DOUBLE)
- nb_kernel_list_add_kernels(kernellist_avx_128_fma_double,kernellist_avx_128_fma_double_size);
+#if (defined GMX_SIMD_X86_AVX_128_FMA && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_avx_128_fma_double, kernellist_avx_128_fma_double_size);
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_256 && defined GMX_DOUBLE)
- nb_kernel_list_add_kernels(kernellist_avx_256_double,kernellist_avx_256_double_size);
+#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_avx_256_double, kernellist_avx_256_double_size);
+#endif
+#if (defined GMX_SIMD_SPARC64_HPC_ACE && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sparc64_hpc_ace_double, kernellist_sparc64_hpc_ace_double_size);
#endif
; /* empty statement to avoid a completely empty block */
}
/* Create a hash for faster lookups */
nb_kernel_list_hash_init();
- nonbonded_setup_done=TRUE;
+ nonbonded_setup_done = TRUE;
}
-#ifdef GMX_THREAD_MPI
tMPI_Thread_mutex_unlock(&nonbonded_setup_mutex);
-#endif
}
void
-gmx_nonbonded_set_kernel_pointers(FILE *log, t_nblist *nl)
+gmx_nonbonded_set_kernel_pointers(FILE *log, t_nblist *nl, gmx_bool bElecAndVdwSwitchDiffers)
{
const char * elec;
const char * elec_mod;
arch_and_padding[] =
{
/* Single precision */
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_256) && !(defined GMX_DOUBLE)
+#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER) && !(defined GMX_DOUBLE)
{ "avx_256_single", 8 },
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
+#if (defined GMX_SIMD_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
{ "avx_128_fma_single", 4 },
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1) && !(defined GMX_DOUBLE)
+#if (defined GMX_SIMD_X86_SSE4_1) && !(defined GMX_DOUBLE)
{ "sse4_1_single", 4 },
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_SSE2) && !(defined GMX_DOUBLE)
+#if (defined GMX_SIMD_X86_SSE2) && !(defined GMX_DOUBLE)
{ "sse2_single", 4 },
#endif
/* Double precision */
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_256 && defined GMX_DOUBLE)
+#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER && defined GMX_DOUBLE)
{ "avx_256_double", 4 },
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA && defined GMX_DOUBLE)
+#if (defined GMX_SIMD_X86_AVX_128_FMA && defined GMX_DOUBLE)
/* Sic. Double precision 2-way SIMD does not require neighbor list padding,
* since the kernels execute a loop unrolled a factor 2, followed by
* a possible single odd-element epilogue.
*/
{ "avx_128_fma_double", 1 },
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_SSE2 && defined GMX_DOUBLE)
+#if (defined GMX_SIMD_X86_SSE2 && defined GMX_DOUBLE)
/* No padding - see comment above */
{ "sse2_double", 1 },
#endif
-#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1 && defined GMX_DOUBLE)
+#if (defined GMX_SIMD_X86_SSE4_1 && defined GMX_DOUBLE)
/* No padding - see comment above */
{ "sse4_1_double", 1 },
+#endif
+#if (defined GMX_SIMD_SPARC64_HPC_ACE && defined GMX_DOUBLE)
+ /* No padding - see comment above */
+ { "sparc64_hpc_ace_double", 1 },
#endif
{ "c", 1 },
};
int narch = asize(arch_and_padding);
int i;
- if(nonbonded_setup_done==FALSE)
+ if (nonbonded_setup_done == FALSE)
{
/* We typically call this setup routine before starting timers,
* but if that has not been done for whatever reason we do it now.
*/
- gmx_nonbonded_setup(NULL,NULL,FALSE);
+ gmx_nonbonded_setup(NULL, FALSE);
}
/* Not used yet */
- other="";
+ other = "";
nl->kernelptr_vf = NULL;
nl->kernelptr_v = NULL;
vdw_mod = eintmod_names[nl->ivdwmod];
geom = gmx_nblist_geometry_names[nl->igeometry];
- if(nl->type==GMX_NBLIST_INTERACTION_ADRESS){
- nl->kernelptr_vf = gmx_nb_generic_adress_kernel;
- nl->kernelptr_f = gmx_nb_generic_adress_kernel;
+ if (nl->type == GMX_NBLIST_INTERACTION_ADRESS)
+ {
+ nl->kernelptr_vf = (void *) gmx_nb_generic_adress_kernel;
+ nl->kernelptr_f = (void *) gmx_nb_generic_adress_kernel;
nl->simd_padding_width = 1;
return;
}
- if(nl->type==GMX_NBLIST_INTERACTION_FREE_ENERGY)
+ if (nl->type == GMX_NBLIST_INTERACTION_FREE_ENERGY)
{
- nl->kernelptr_vf = gmx_nb_free_energy_kernel;
- nl->kernelptr_f = gmx_nb_free_energy_kernel;
+ nl->kernelptr_vf = (void *) gmx_nb_free_energy_kernel;
+ nl->kernelptr_f = (void *) gmx_nb_free_energy_kernel;
nl->simd_padding_width = 1;
}
- else if(!gmx_strcasecmp_min(geom,"CG-CG"))
+ else if (!gmx_strcasecmp_min(geom, "CG-CG"))
{
- nl->kernelptr_vf = gmx_nb_generic_cg_kernel;
- nl->kernelptr_f = gmx_nb_generic_cg_kernel;
+ nl->kernelptr_vf = (void *) gmx_nb_generic_cg_kernel;
+ nl->kernelptr_f = (void *) gmx_nb_generic_cg_kernel;
nl->simd_padding_width = 1;
}
else
{
/* Try to find a specific kernel first */
- for(i=0;i<narch && nl->kernelptr_vf==NULL ;i++)
+ for (i = 0; i < narch && nl->kernelptr_vf == NULL; i++)
{
- nl->kernelptr_vf = nb_kernel_list_findkernel(log,arch_and_padding[i].arch,elec,elec_mod,vdw,vdw_mod,geom,other,"PotentialAndForce");
+ nl->kernelptr_vf = (void *) nb_kernel_list_findkernel(log, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "PotentialAndForce");
nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
}
- for(i=0;i<narch && nl->kernelptr_f==NULL ;i++)
+ for (i = 0; i < narch && nl->kernelptr_f == NULL; i++)
{
- nl->kernelptr_f = nb_kernel_list_findkernel(log,arch_and_padding[i].arch,elec,elec_mod,vdw,vdw_mod,geom,other,"Force");
+ nl->kernelptr_f = (void *) nb_kernel_list_findkernel(log, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "Force");
nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
/* If there is not force-only optimized kernel, is there a potential & force one? */
- if(nl->kernelptr_f == NULL)
+ if (nl->kernelptr_f == NULL)
{
- nl->kernelptr_f = nb_kernel_list_findkernel(NULL,arch_and_padding[i].arch,elec,elec_mod,vdw,vdw_mod,geom,other,"PotentialAndForce");
+ nl->kernelptr_f = (void *) nb_kernel_list_findkernel(NULL, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "PotentialAndForce");
nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
}
}
-
- /* Give up, pick a generic one instead */
- if(nl->kernelptr_vf==NULL)
+
+ /* For now, the accelerated kernels cannot handle the combination of switch functions for both
+ * electrostatics and VdW that use different switch radius or switch cutoff distances
+ * (both of them enter in the switch function calculation). This would require
+ * us to evaluate two completely separate switch functions for every interaction.
+ * Instead, we disable such kernels by setting the pointer to NULL.
+ * This will cause the generic kernel (which can handle it) to be called instead.
+ *
+ * Note that we typically already enable tabulated coulomb interactions for this case,
+ * so this is mostly a safe-guard to make sure we call the generic kernel if the
+ * tables are disabled.
+ */
+ if ((nl->ielec != GMX_NBKERNEL_ELEC_NONE) && (nl->ielecmod == eintmodPOTSWITCH) &&
+ (nl->ivdw != GMX_NBKERNEL_VDW_NONE) && (nl->ivdwmod == eintmodPOTSWITCH) &&
+ bElecAndVdwSwitchDiffers)
{
- nl->kernelptr_vf = gmx_nb_generic_kernel;
- nl->kernelptr_f = gmx_nb_generic_kernel;
+ nl->kernelptr_vf = NULL;
+ nl->kernelptr_f = NULL;
+ }
+
+ /* Give up, pick a generic one instead.
+ * We only do this for particle-particle kernels; by leaving the water-optimized kernel
+ * pointers to NULL, the water optimization will automatically be disabled for this interaction.
+ */
+ if (nl->kernelptr_vf == NULL && !gmx_strcasecmp_min(geom, "Particle-Particle"))
+ {
+ nl->kernelptr_vf = (void *) gmx_nb_generic_kernel;
+ nl->kernelptr_f = (void *) gmx_nb_generic_kernel;
nl->simd_padding_width = 1;
- if(debug)
+ if (debug)
{
fprintf(debug,
"WARNING - Slow generic NB kernel used for neighborlist with\n"
" Elec: '%s', Modifier: '%s'\n"
- " Vdw: '%s', Modifier: '%s'\n"
- " Geom: '%s', Other: '%s'\n\n",
- elec,elec_mod,vdw,vdw_mod,geom,other);
+ " Vdw: '%s', Modifier: '%s'\n",
+ elec, elec_mod, vdw, vdw_mod);
}
}
}
-
return;
}
-void do_nonbonded(t_commrec *cr,t_forcerec *fr,
- rvec x[],rvec f_shortrange[],rvec f_longrange[],t_mdatoms *mdatoms,t_blocka *excl,
- gmx_grppairener_t *grppener,rvec box_size,
- t_nrnb *nrnb,real *lambda, real *dvdl,
- int nls,int eNL,int flags)
+void do_nonbonded(t_forcerec *fr,
+ rvec x[], rvec f_shortrange[], rvec f_longrange[], t_mdatoms *mdatoms, t_blocka *excl,
+ gmx_grppairener_t *grppener,
+ t_nrnb *nrnb, real *lambda, real *dvdl,
+ int nls, int eNL, int flags)
{
- t_nblist * nlist;
- int n,n0,n1,i,i0,i1,sz,range;
- t_nblists * nblists;
+ t_nblist * nlist;
+ int n, n0, n1, i, i0, i1, sz, range;
+ t_nblists * nblists;
nb_kernel_data_t kernel_data;
- nb_kernel_t * kernelptr=NULL;
+ nb_kernel_t * kernelptr = NULL;
rvec * f;
-
+
kernel_data.flags = flags;
kernel_data.exclusions = excl;
kernel_data.lambda = lambda;
kernel_data.dvdl = dvdl;
-
- if(fr->bAllvsAll)
+
+ if (fr->bAllvsAll)
{
+ gmx_incons("All-vs-all kernels have not been implemented in version 4.6");
return;
}
-
+
if (eNL >= 0)
{
- i0 = eNL;
- i1 = i0+1;
+ i0 = eNL;
+ i1 = i0+1;
+ }
+ else
+ {
+ i0 = 0;
+ i1 = eNL_NR;
+ }
+
+ if (nls >= 0)
+ {
+ n0 = nls;
+ n1 = nls+1;
}
else
{
- i0 = 0;
- i1 = eNL_NR;
- }
-
- if (nls >= 0)
- {
- n0 = nls;
- n1 = nls+1;
- }
- else
- {
- n0 = 0;
- n1 = fr->nnblists;
- }
-
- for(n=n0; (n<n1); n++)
- {
- nblists = &fr->nblists[n];
+ n0 = 0;
+ n1 = fr->nnblists;
+ }
+
+ for (n = n0; (n < n1); n++)
+ {
+ nblists = &fr->nblists[n];
kernel_data.table_elec = &nblists->table_elec;
kernel_data.table_vdw = &nblists->table_vdw;
kernel_data.table_elec_vdw = &nblists->table_elec_vdw;
- for(range=0;range<2;range++)
+ for (range = 0; range < 2; range++)
{
/* Are we doing short/long-range? */
- if(range==0)
+ if (range == 0)
{
/* Short-range */
- if(!(flags & GMX_NONBONDED_DO_SR))
+ if (!(flags & GMX_NONBONDED_DO_SR))
{
continue;
}
nlist = nblists->nlist_sr;
f = f_shortrange;
}
- else if(range==1)
+ else
{
/* Long-range */
- if(!(flags & GMX_NONBONDED_DO_LR))
+ if (!(flags & GMX_NONBONDED_DO_LR))
{
continue;
}
f = f_longrange;
}
- for(i=i0; (i<i1); i++)
+ for (i = i0; (i < i1); i++)
{
if (nlist[i].nri > 0)
{
- if(flags & GMX_NONBONDED_DO_POTENTIAL)
+ if (flags & GMX_NONBONDED_DO_POTENTIAL)
{
/* Potential and force */
kernelptr = (nb_kernel_t *)nlist[i].kernelptr_vf;
kernelptr = (nb_kernel_t *)nlist[i].kernelptr_f;
}
- if(nlist[i].type!=GMX_NBLIST_INTERACTION_FREE_ENERGY && (flags & GMX_NONBONDED_DO_FOREIGNLAMBDA))
+ if (nlist[i].type != GMX_NBLIST_INTERACTION_FREE_ENERGY && (flags & GMX_NONBONDED_DO_FOREIGNLAMBDA))
{
/* We don't need the non-perturbed interactions */
continue;
}
- (*kernelptr)(&(nlist[i]),x,f,fr,mdatoms,&kernel_data,nrnb);
- }
+ /* Neighborlists whose kernelptr==NULL will always be empty */
+ if (kernelptr != NULL)
+ {
+ (*kernelptr)(&(nlist[i]), x, f, fr, mdatoms, &kernel_data, nrnb);
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Non-empty neighborlist does not have any kernel pointer assigned.");
+ }
+ }
}
}
}
}
static void
-nb_listed_warning_rlimit(const rvec *x,int ai, int aj,int * global_atom_index,real r, real rlimit)
+nb_listed_warning_rlimit(const rvec *x, int ai, int aj, int * global_atom_index, real r, real rlimit)
{
gmx_warning("Listed nonbonded interaction between particles %d and %d\n"
"at distance %.3f which is larger than the table limit %.3f nm.\n\n"
"IMPORTANT: This should not happen in a stable simulation, so there is\n"
"probably something wrong with your system. Only change the table-extension\n"
"distance in the mdp file if you are really sure that is the reason.\n",
- glatnr(global_atom_index,ai),glatnr(global_atom_index,aj),r,rlimit);
+ glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r, rlimit);
if (debug)
{
fprintf(debug,
"%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. Ignored\n",
- x[ai][XX],x[ai][YY],x[ai][ZZ],x[aj][XX],x[aj][YY],x[aj][ZZ],
- glatnr(global_atom_index,ai),glatnr(global_atom_index,aj),r);
+ x[ai][XX], x[ai][YY], x[ai][ZZ], x[aj][XX], x[aj][YY], x[aj][ZZ],
+ glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r);
}
}
* extra functional call for every single pair listed in the topology.
*/
static real
-nb_evaluate_single(real r2, real tabscale,real *vftab,
+nb_evaluate_single(real r2, real tabscale, real *vftab,
real qq, real c6, real c12, real *velec, real *vvdw)
{
- real rinv,r,rtab,eps,eps2,Y,F,Geps,Heps2,Fp,VVe,FFe,VVd,FFd,VVr,FFr,fscal;
+ real rinv, r, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VVe, FFe, VVd, FFd, VVr, FFr, fscal;
int ntab;
/* Do the tabulated interactions - first table lookup */
real
-do_nonbonded_listed(int ftype,int nbonds,
- const t_iatom iatoms[],const t_iparams iparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real *lambda, real *dvdl,
- const t_mdatoms *md,
- const t_forcerec *fr,gmx_grppairener_t *grppener,
- int *global_atom_index)
+do_nonbonded_listed(int ftype, int nbonds,
+ const t_iatom iatoms[], const t_iparams iparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const t_pbc *pbc, const t_graph *g,
+ real *lambda, real *dvdl,
+ const t_mdatoms *md,
+ const t_forcerec *fr, gmx_grppairener_t *grppener,
+ int *global_atom_index)
{
- int ielec,ivdw;
- real qq,c6,c12;
+ int ielec, ivdw;
+ real qq, c6, c12;
rvec dx;
ivec dt;
- int i,j,itype,ai,aj,gid;
+ int i, j, itype, ai, aj, gid;
int fshift_index;
- real r2,rinv;
- real fscal,velec,vvdw;
+ real r2, rinv;
+ real fscal, velec, vvdw;
real * energygrp_elec;
real * energygrp_vdw;
- static gmx_bool warned_rlimit=FALSE;
+ static gmx_bool warned_rlimit = FALSE;
/* Free energy stuff */
gmx_bool bFreeEnergy;
- real LFC[2],LFV[2],DLF[2],lfac_coul[2],lfac_vdw[2],dlfac_coul[2],dlfac_vdw[2];
- real qqB,c6B,c12B,sigma2_def,sigma2_min;
-
-
- switch (ftype) {
+ real LFC[2], LFV[2], DLF[2], lfac_coul[2], lfac_vdw[2], dlfac_coul[2], dlfac_vdw[2];
+ real qqB, c6B, c12B, sigma2_def, sigma2_min;
+
+
+ switch (ftype)
+ {
case F_LJ14:
case F_LJC14_Q:
energygrp_elec = grppener->ener[egCOUL14];
default:
energygrp_elec = NULL; /* Keep compiler happy */
energygrp_vdw = NULL; /* Keep compiler happy */
- gmx_fatal(FARGS,"Unknown function type %d in do_nonbonded14",ftype);
+ gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", ftype);
break;
}
-
- if(fr->efep != efepNO)
+
+ if (fr->efep != efepNO)
{
/* Lambda factor for state A=1-lambda and B=lambda */
LFC[0] = 1.0 - lambda[efptCOUL];
DLF[1] = 1;
/* precalculate */
- sigma2_def = pow(fr->sc_sigma6_def,1.0/3.0);
- sigma2_min = pow(fr->sc_sigma6_min,1.0/3.0);
+ sigma2_def = pow(fr->sc_sigma6_def, 1.0/3.0);
+ sigma2_min = pow(fr->sc_sigma6_min, 1.0/3.0);
- for (i=0;i<2;i++)
+ for (i = 0; i < 2; i++)
{
- lfac_coul[i] = (fr->sc_power==2 ? (1-LFC[i])*(1-LFC[i]) : (1-LFC[i]));
- dlfac_coul[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power==2 ? (1-LFC[i]) : 1);
- lfac_vdw[i] = (fr->sc_power==2 ? (1-LFV[i])*(1-LFV[i]) : (1-LFV[i]));
- dlfac_vdw[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power==2 ? (1-LFV[i]) : 1);
+ lfac_coul[i] = (fr->sc_power == 2 ? (1-LFC[i])*(1-LFC[i]) : (1-LFC[i]));
+ dlfac_coul[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFC[i]) : 1);
+ lfac_vdw[i] = (fr->sc_power == 2 ? (1-LFV[i])*(1-LFV[i]) : (1-LFV[i]));
+ dlfac_vdw[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFV[i]) : 1);
}
}
else
}
bFreeEnergy = FALSE;
- for(i=0; (i<nbonds); )
+ for (i = 0; (i < nbonds); )
{
itype = iatoms[i++];
ai = iatoms[i++];
aj = iatoms[i++];
- gid = GID(md->cENER[ai],md->cENER[aj],md->nenergrp);
-
+ gid = GID(md->cENER[ai], md->cENER[aj], md->nenergrp);
+
/* Get parameters */
- switch (ftype) {
+ switch (ftype)
+ {
case F_LJ14:
bFreeEnergy =
- (fr->efep != efepNO &&
- ((md->nPerturbed && (md->bPerturbed[ai] || md->bPerturbed[aj])) ||
- iparams[itype].lj14.c6A != iparams[itype].lj14.c6B ||
- iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
+ (fr->efep != efepNO &&
+ ((md->nPerturbed && (md->bPerturbed[ai] || md->bPerturbed[aj])) ||
+ iparams[itype].lj14.c6A != iparams[itype].lj14.c6B ||
+ iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
qq = md->chargeA[ai]*md->chargeA[aj]*fr->epsfac*fr->fudgeQQ;
c6 = iparams[itype].lj14.c6A;
c12 = iparams[itype].lj14.c12A;
qq = c6 = c12 = 0; /* Keep compiler happy */
break;
}
-
+
/* To save flops in the optimized kernels, c6/c12 have 6.0/12.0 derivative prefactors
* included in the general nfbp array now. This means the tables are scaled down by the
* same factor, so when we use the original c6/c12 parameters from iparams[] they must
*/
c6 *= 6.0;
c12 *= 12.0;
-
+
/* Do we need to apply full periodic boundary conditions? */
- if(fr->bMolPBC==TRUE)
+ if (fr->bMolPBC == TRUE)
{
- fshift_index = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
+ fshift_index = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
}
else
{
fshift_index = CENTRAL;
- rvec_sub(x[ai],x[aj],dx);
+ rvec_sub(x[ai], x[aj], dx);
}
r2 = norm2(dx);
- if(r2>=fr->tab14.r*fr->tab14.r)
+ if (r2 >= fr->tab14.r*fr->tab14.r)
{
- if(warned_rlimit==FALSE)
+ /* This check isn't race free. But it doesn't matter because if a race occurs the only
+ * disadvantage is that the warning is printed twice */
+ if (warned_rlimit == FALSE)
{
- nb_listed_warning_rlimit(x,ai,aj,global_atom_index,sqrt(r2),fr->tab14.r);
- warned_rlimit=TRUE;
+ nb_listed_warning_rlimit(x, ai, aj, global_atom_index, sqrt(r2), fr->tab14.r);
+ warned_rlimit = TRUE;
}
continue;
}
c6B = iparams[itype].lj14.c6B*6.0;
c12B = iparams[itype].lj14.c12B*12.0;
- fscal = nb_free_energy_evaluate_single(r2,fr->sc_r_power,fr->sc_alphacoul,fr->sc_alphavdw,
- fr->tab14.scale,fr->tab14.data,qq,c6,c12,qqB,c6B,c12B,
- LFC,LFV,DLF,lfac_coul,lfac_vdw,dlfac_coul,dlfac_vdw,
- fr->sc_sigma6_def,fr->sc_sigma6_min,sigma2_def,sigma2_min,&velec,&vvdw,dvdl);
+ fscal = nb_free_energy_evaluate_single(r2, fr->sc_r_power, fr->sc_alphacoul, fr->sc_alphavdw,
+ fr->tab14.scale, fr->tab14.data, qq, c6, c12, qqB, c6B, c12B,
+ LFC, LFV, DLF, lfac_coul, lfac_vdw, dlfac_coul, dlfac_vdw,
+ fr->sc_sigma6_def, fr->sc_sigma6_min, sigma2_def, sigma2_min, &velec, &vvdw, dvdl);
}
else
{
/* Evaluate tabulated interaction without free energy */
- fscal = nb_evaluate_single(r2,fr->tab14.scale,fr->tab14.data,qq,c6,c12,&velec,&vvdw);
+ fscal = nb_evaluate_single(r2, fr->tab14.scale, fr->tab14.data, qq, c6, c12, &velec, &vvdw);
}
energygrp_elec[gid] += velec;
energygrp_vdw[gid] += vvdw;
- svmul(fscal,dx,dx);
+ svmul(fscal, dx, dx);
/* Add the forces */
- rvec_inc(f[ai],dx);
- rvec_dec(f[aj],dx);
+ rvec_inc(f[ai], dx);
+ rvec_dec(f[aj], dx);
if (g)
{
/* Correct the shift forces using the graph */
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
fshift_index = IVEC2IS(dt);
}
- if(fshift_index!=CENTRAL)
+ if (fshift_index != CENTRAL)
{
- rvec_inc(fshift[fshift_index],dx);
- rvec_dec(fshift[CENTRAL],dx);
+ rvec_inc(fshift[fshift_index], dx);
+ rvec_dec(fshift[CENTRAL], dx);
}
}
return 0.0;
}
-
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff