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Commit bf6d95c2 authored by John Chodera (MSKCC)'s avatar John Chodera (MSKCC)
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Merge remote-tracking branch 'upstream/master'

parents 896413aa 227c86bf
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Showing with 1495 additions and 1527 deletions
CMakeLists.txt
View file @ bf6d95c2
...@@ -81,20 +81,6 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT}) ...@@ -81,20 +81,6 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/validate libraries/irrxml) SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/validate libraries/irrxml)
IF(WIN32) IF(WIN32)
SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/pthreads) SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/pthreads)
ADD_CUSTOM_TARGET(PthreadsLibraries ALL)
FILE(GLOB PTHREADS_LIBRARIES libraries/pthreads/lib/*.dll libraries/pthreads/lib/*.lib)
ADD_CUSTOM_COMMAND(TARGET PthreadsLibraries COMMAND ${CMAKE_COMMAND} ARGS -E make_directory "${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_CFG_INTDIR}/")
FOREACH(lib ${PTHREADS_LIBRARIES})
ADD_CUSTOM_COMMAND(TARGET PthreadsLibraries COMMAND ${CMAKE_COMMAND} ARGS -E copy ${lib} "${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_CFG_INTDIR}/")
INSTALL(FILES ${lib} DESTINATION "lib/")
ENDFOREACH(lib)
LINK_DIRECTORIES("${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_CFG_INTDIR}")
IF(CMAKE_SIZEOF_VOID_P EQUAL 8)
SET(PTHREADS_LIB pthreadVC2_x64)
ELSE(CMAKE_SIZEOF_VOID_P EQUAL 8)
SET(PTHREADS_LIB pthreadVC2)
SET(PTHREADS_LIB_STATIC pthreadVC2_static_mt)
ENDIF(CMAKE_SIZEOF_VOID_P EQUAL 8)
ELSE(WIN32) ELSE(WIN32)
IF (NOT ANDROID) IF (NOT ANDROID)
SET(PTHREADS_LIB pthread) SET(PTHREADS_LIB pthread)
...@@ -303,17 +289,14 @@ ENDIF (CMAKE_SYSTEM_NAME MATCHES "Linux") ...@@ -303,17 +289,14 @@ ENDIF (CMAKE_SYSTEM_NAME MATCHES "Linux")
IF(OPENMM_BUILD_SHARED_LIB) IF(OPENMM_BUILD_SHARED_LIB)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES}) ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY") SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY -DPTHREAD_BUILDING_SHARED_LIBRARY")
IF(WIN32)
ADD_DEPENDENCIES(${SHARED_TARGET} PthreadsLibraries)
ENDIF(WIN32)
ENDIF(OPENMM_BUILD_SHARED_LIB) ENDIF(OPENMM_BUILD_SHARED_LIB)
SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries") SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
IF(OPENMM_BUILD_STATIC_LIB) IF(OPENMM_BUILD_STATIC_LIB)
ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES}) ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DLEPTON_USE_STATIC_LIBRARIES -DPTW32_STATIC_LIB") SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DLEPTON_USE_STATIC_LIBRARIES -DPTW32_STATIC_LIB")
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY") SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY -DPTHREAD_BUILDING_STATIC_LIBRARY")
ENDIF(OPENMM_BUILD_STATIC_LIB) ENDIF(OPENMM_BUILD_STATIC_LIB)
IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS) IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
......
cmake_modules/FindOpenCL.cmake
View file @ bf6d95c2
...@@ -33,6 +33,7 @@ find_path(OPENCL_INCLUDE_DIR ...@@ -33,6 +33,7 @@ find_path(OPENCL_INCLUDE_DIR
"/usr/local/cuda" "/usr/local/cuda"
"/usr/local/streamsdk" "/usr/local/streamsdk"
"/usr" "/usr"
"${CUDA_TOOLKIT_ROOT_DIR}"
PATH_SUFFIXES "include" PATH_SUFFIXES "include"
) )
......
docs-source/usersguide/application.rst
View file @ bf6d95c2
...@@ -1121,6 +1121,25 @@ integrator is: ...@@ -1121,6 +1121,25 @@ integrator is:
The parameter is the integration error tolerance (0.001), whose meaning is the The parameter is the integration error tolerance (0.001), whose meaning is the
same as for the Langevin integrator. same as for the Langevin integrator.
Multiple Time Step Integrator
-----------------------------
The :class:`MTSIntegrator` class implements the rRESPA multiple time step
algorithm\ :cite:`Tuckerman1992`. This allows some forces in the system to be evaluated more
frequently than others. For details on how to use it, consult the API
documentation.
aMD Integrator
--------------
There are three different integrator types that implement variations of the
aMD\ :cite:`Hamelberg2007` accelerated sampling algorithm: :class:`AMDIntegrator`,
:class:`AMDForceGroupIntegrator`, and :class:`DualAMDIntegrator`. They
perform integration on a modified potential energy surface to allow much faster
sampling of conformations. For details on how to use them, consult the API
documentation.
Temperature Coupling Temperature Coupling
==================== ====================
......
docs-source/usersguide/references.bib
View file @ bf6d95c2
...@@ -90,6 +90,17 @@ ...@@ -90,6 +90,17 @@
type = {Journal Article} type = {Journal Article}
} }
@article{Hamelberg2007,
author={Hamelberg, Donald and de Oliveira, Cesar Augusto F. and McCammon, J. Andrew},
title={Sampling of slow diffusive conformational transitions with accelerated molecular dynamics},
journal={Journal of Chemical Physics},
volume={127},
number={15},
pages={155102},
year={2007},
type = {Journal Article}
}
@article{Hawkins1995 @article{Hawkins1995
author = {Hawkins, Gregory D. and Cramer, Christopher J. and Truhlar, Donald G.}, author = {Hawkins, Gregory D. and Cramer, Christopher J. and Truhlar, Donald G.},
title = {Pairwise solute descreening of solute charges from a dielectric medium}, title = {Pairwise solute descreening of solute charges from a dielectric medium},
...@@ -440,6 +451,17 @@ ...@@ -440,6 +451,17 @@
type = {Journal Article} type = {Journal Article}
} }
@article{Tuckerman1992,
author={Tuckerman, M. and Berne, Bruce J. and Martyna, Glenn J.},
title={Reversible multiple time scale molecular dynamics},
journal = {Journal of Chemical Physics},
volume={97},
number={3},
pages={1990-2001},
year={1992},
type = {Journal Article}
}
@article{Uberuaga2004, @article{Uberuaga2004,
author = {Blas P. Uberuaga and Marian Anghel and Arthur author = {Blas P. Uberuaga and Marian Anghel and Arthur
F. Voter}, F. Voter},
......
libraries/pthreads/include/pthread.h
View file @ bf6d95c2
This diff is collapsed.
libraries/pthreads/include/sched.h deleted 100644 → 0
View file @ 896413aa
/*
* Module: sched.h
*
* Purpose:
* Provides an implementation of POSIX realtime extensions
* as defined in
*
* POSIX 1003.1b-1993 (POSIX.1b)
*
* --------------------------------------------------------------------------
*
* Pthreads-win32 - POSIX Threads Library for Win32
* Copyright(C) 1998 John E. Bossom
* Copyright(C) 1999,2005 Pthreads-win32 contributors
*
* Contact Email: rpj@callisto.canberra.edu.au
*
* The current list of contributors is contained
* in the file CONTRIBUTORS included with the source
* code distribution. The list can also be seen at the
* following World Wide Web location:
* http://sources.redhat.com/pthreads-win32/contributors.html
*
* This library 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 of the License, or (at your option) any later version.
*
* This library 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 this library in the file COPYING.LIB;
* if not, write to the Free Software Foundation, Inc.,
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA
*/
#ifndef _SCHED_H
#define _SCHED_H
#undef PTW32_LEVEL
#if defined(_POSIX_SOURCE)
#define PTW32_LEVEL 0
/* Early POSIX */
#endif
#if defined(_POSIX_C_SOURCE) && _POSIX_C_SOURCE >= 199309
#undef PTW32_LEVEL
#define PTW32_LEVEL 1
/* Include 1b, 1c and 1d */
#endif
#if defined(INCLUDE_NP)
#undef PTW32_LEVEL
#define PTW32_LEVEL 2
/* Include Non-Portable extensions */
#endif
#define PTW32_LEVEL_MAX 3
#if !defined(PTW32_LEVEL)
#define PTW32_LEVEL PTW32_LEVEL_MAX
/* Include everything */
#endif
#if __GNUC__ && ! defined (__declspec)
# error Please upgrade your GNU compiler to one that supports __declspec.
#endif
/*
* When building the DLL code, you should define PTW32_BUILD so that
* the variables/functions are exported correctly. When using the DLL,
* do NOT define PTW32_BUILD, and then the variables/functions will
* be imported correctly.
*/
#ifndef PTW32_STATIC_LIB
# ifdef PTW32_BUILD
# define PTW32_DLLPORT __declspec (dllexport)
# else
# define PTW32_DLLPORT __declspec (dllimport)
# endif
#else
# define PTW32_DLLPORT
#endif
/*
* This is a duplicate of what is in the autoconf config.h,
* which is only used when building the pthread-win32 libraries.
*/
#ifndef PTW32_CONFIG_H
# if defined(WINCE)
# define NEED_ERRNO
# define NEED_SEM
# endif
# if defined(_UWIN) || defined(__MINGW32__)
# define HAVE_MODE_T
# endif
#endif
/*
*
*/
#if PTW32_LEVEL >= PTW32_LEVEL_MAX
#ifdef NEED_ERRNO
#include "need_errno.h"
#else
#include <errno.h>
#endif
#endif /* PTW32_LEVEL >= PTW32_LEVEL_MAX */
#if defined(__MINGW32__) || defined(_UWIN)
#if PTW32_LEVEL >= PTW32_LEVEL_MAX
/* For pid_t */
# include <sys/types.h>
/* Required by Unix 98 */
# include <time.h>
#endif /* PTW32_LEVEL >= PTW32_LEVEL_MAX */
#else
typedef int pid_t;
#endif
/* Thread scheduling policies */
enum {
SCHED_OTHER = 0,
SCHED_FIFO,
SCHED_RR,
SCHED_MIN = SCHED_OTHER,
SCHED_MAX = SCHED_RR
};
struct sched_param {
int sched_priority;
};
#ifdef __cplusplus
extern "C"
{
#endif /* __cplusplus */
PTW32_DLLPORT int __cdecl sched_yield (void);
PTW32_DLLPORT int __cdecl sched_get_priority_min (int policy);
PTW32_DLLPORT int __cdecl sched_get_priority_max (int policy);
PTW32_DLLPORT int __cdecl sched_setscheduler (pid_t pid, int policy);
PTW32_DLLPORT int __cdecl sched_getscheduler (pid_t pid);
/*
* Note that this macro returns ENOTSUP rather than
* ENOSYS as might be expected. However, returning ENOSYS
* should mean that sched_get_priority_{min,max} are
* not implemented as well as sched_rr_get_interval.
* This is not the case, since we just don't support
* round-robin scheduling. Therefore I have chosen to
* return the same value as sched_setscheduler when
* SCHED_RR is passed to it.
*/
#define sched_rr_get_interval(_pid, _interval) \
( errno = ENOTSUP, (int) -1 )
#ifdef __cplusplus
} /* End of extern "C" */
#endif /* __cplusplus */
#undef PTW32_LEVEL
#undef PTW32_LEVEL_MAX
#endif /* !_SCHED_H */
libraries/pthreads/include/semaphore.h deleted 100644 → 0
View file @ 896413aa
/*
* Module: semaphore.h
*
* Purpose:
* Semaphores aren't actually part of the PThreads standard.
* They are defined by the POSIX Standard:
*
* POSIX 1003.1b-1993 (POSIX.1b)
*
* --------------------------------------------------------------------------
*
* Pthreads-win32 - POSIX Threads Library for Win32
* Copyright(C) 1998 John E. Bossom
* Copyright(C) 1999,2005 Pthreads-win32 contributors
*
* Contact Email: rpj@callisto.canberra.edu.au
*
* The current list of contributors is contained
* in the file CONTRIBUTORS included with the source
* code distribution. The list can also be seen at the
* following World Wide Web location:
* http://sources.redhat.com/pthreads-win32/contributors.html
*
* This library 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 of the License, or (at your option) any later version.
*
* This library 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 this library in the file COPYING.LIB;
* if not, write to the Free Software Foundation, Inc.,
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA
*/
#if !defined( SEMAPHORE_H )
#define SEMAPHORE_H
#undef PTW32_LEVEL
#if defined(_POSIX_SOURCE)
#define PTW32_LEVEL 0
/* Early POSIX */
#endif
#if defined(_POSIX_C_SOURCE) && _POSIX_C_SOURCE >= 199309
#undef PTW32_LEVEL
#define PTW32_LEVEL 1
/* Include 1b, 1c and 1d */
#endif
#if defined(INCLUDE_NP)
#undef PTW32_LEVEL
#define PTW32_LEVEL 2
/* Include Non-Portable extensions */
#endif
#define PTW32_LEVEL_MAX 3
#if !defined(PTW32_LEVEL)
#define PTW32_LEVEL PTW32_LEVEL_MAX
/* Include everything */
#endif
#if __GNUC__ && ! defined (__declspec)
# error Please upgrade your GNU compiler to one that supports __declspec.
#endif
/*
* When building the DLL code, you should define PTW32_BUILD so that
* the variables/functions are exported correctly. When using the DLL,
* do NOT define PTW32_BUILD, and then the variables/functions will
* be imported correctly.
*/
#ifndef PTW32_STATIC_LIB
# ifdef PTW32_BUILD
# define PTW32_DLLPORT __declspec (dllexport)
# else
# define PTW32_DLLPORT __declspec (dllimport)
# endif
#else
# define PTW32_DLLPORT
#endif
/*
* This is a duplicate of what is in the autoconf config.h,
* which is only used when building the pthread-win32 libraries.
*/
#ifndef PTW32_CONFIG_H
# if defined(WINCE)
# define NEED_ERRNO
# define NEED_SEM
# endif
# if defined(_UWIN) || defined(__MINGW32__)
# define HAVE_MODE_T
# endif
#endif
/*
*
*/
#if PTW32_LEVEL >= PTW32_LEVEL_MAX
#ifdef NEED_ERRNO
#include "need_errno.h"
#else
#include <errno.h>
#endif
#endif /* PTW32_LEVEL >= PTW32_LEVEL_MAX */
#define _POSIX_SEMAPHORES
#ifdef __cplusplus
extern "C"
{
#endif /* __cplusplus */
#ifndef HAVE_MODE_T
typedef unsigned int mode_t;
#endif
typedef struct sem_t_ * sem_t;
PTW32_DLLPORT int __cdecl sem_init (sem_t * sem,
int pshared,
unsigned int value);
PTW32_DLLPORT int __cdecl sem_destroy (sem_t * sem);
PTW32_DLLPORT int __cdecl sem_trywait (sem_t * sem);
PTW32_DLLPORT int __cdecl sem_wait (sem_t * sem);
PTW32_DLLPORT int __cdecl sem_timedwait (sem_t * sem,
const struct timespec * abstime);
PTW32_DLLPORT int __cdecl sem_post (sem_t * sem);
PTW32_DLLPORT int __cdecl sem_post_multiple (sem_t * sem,
int count);
PTW32_DLLPORT int __cdecl sem_open (const char * name,
int oflag,
mode_t mode,
unsigned int value);
PTW32_DLLPORT int __cdecl sem_close (sem_t * sem);
PTW32_DLLPORT int __cdecl sem_unlink (const char * name);
PTW32_DLLPORT int __cdecl sem_getvalue (sem_t * sem,
int * sval);
#ifdef __cplusplus
} /* End of extern "C" */
#endif /* __cplusplus */
#undef PTW32_LEVEL
#undef PTW32_LEVEL_MAX
#endif /* !SEMAPHORE_H */
libraries/pthreads/src/pthread.cpp 0 → 100644
View file @ bf6d95c2
#include "pthread.h"
PTHREAD_EXPORT volatile long _pthread_cancelling;
PTHREAD_EXPORT int _pthread_concur;
/* Will default to zero as needed */
PTHREAD_EXPORT pthread_once_t _pthread_tls_once;
PTHREAD_EXPORT DWORD _pthread_tls;
/* Note initializer is zero, so this works */
PTHREAD_EXPORT pthread_rwlock_t _pthread_key_lock;
PTHREAD_EXPORT long _pthread_key_max;
PTHREAD_EXPORT long _pthread_key_sch;
PTHREAD_EXPORT void (**_pthread_key_dest)(void *);
platforms/cpu/include/CpuNonbondedForce.h
View file @ bf6d95c2
/* Portions copyright (c) 2006-2013 Stanford University and Simbios. /* Portions copyright (c) 2006-2015 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -174,8 +174,8 @@ protected: ...@@ -174,8 +174,8 @@ protected:
float alphaEwald; float alphaEwald;
int numRx, numRy, numRz; int numRx, numRy, numRz;
int meshDim[3]; int meshDim[3];
std::vector<float> ewaldScaleTable; std::vector<float> erfcTable, ewaldScaleTable;
float ewaldDX, ewaldDXInv; float ewaldDX, ewaldDXInv, erfcDXInv;
std::vector<double> threadEnergy; std::vector<double> threadEnergy;
// The following variables are used to make information accessible to the individual threads. // The following variables are used to make information accessible to the individual threads.
int numberOfAtoms; int numberOfAtoms;
...@@ -241,7 +241,7 @@ protected: ...@@ -241,7 +241,7 @@ protected:
/** /**
* Compute a fast approximation to erfc(x). * Compute a fast approximation to erfc(x).
*/ */
static float erfcApprox(float x); float erfcApprox(float x);
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/cpu/include/CpuNonbondedForceVec4.h
View file @ bf6d95c2
/* Portions copyright (c) 2006-2014 Stanford University and Simbios. /* Portions copyright (c) 2006-2015 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -87,7 +87,7 @@ protected: ...@@ -87,7 +87,7 @@ protected:
/** /**
* Compute a fast approximation to erfc(x). * Compute a fast approximation to erfc(x).
*/ */
static fvec4 erfcApprox(const fvec4& x); fvec4 erfcApprox(const fvec4& x);
/** /**
* Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI) * Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
......
platforms/cpu/include/CpuNonbondedForceVec8.h
View file @ bf6d95c2
/* Portions copyright (c) 2006-2014 Stanford University and Simbios. /* Portions copyright (c) 2006-2015 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -86,7 +86,7 @@ protected: ...@@ -86,7 +86,7 @@ protected:
/** /**
* Compute a fast approximation to erfc(x). * Compute a fast approximation to erfc(x).
*/ */
static fvec8 erfcApprox(const fvec8& x); fvec8 erfcApprox(const fvec8& x);
/** /**
* Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI) * Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
......
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ bf6d95c2
...@@ -171,17 +171,20 @@ void CpuNonbondedForce::setUseSwitchingFunction(float distance) { ...@@ -171,17 +171,20 @@ void CpuNonbondedForce::setUseSwitchingFunction(float distance) {
} }
void CpuNonbondedForce::tabulateEwaldScaleFactor() { void CpuNonbondedForce::tabulateEwaldScaleFactor() {
if (tableIsValid) if (tableIsValid)
return; return;
tableIsValid = true; tableIsValid = true;
ewaldDX = cutoffDistance/NUM_TABLE_POINTS; ewaldDX = cutoffDistance/NUM_TABLE_POINTS;
ewaldDXInv = 1.0f/ewaldDX; ewaldDXInv = 1.0f/ewaldDX;
erfcDXInv = 1.0f/(ewaldDX*alphaEwald);
erfcTable.resize(NUM_TABLE_POINTS+4);
ewaldScaleTable.resize(NUM_TABLE_POINTS+4); ewaldScaleTable.resize(NUM_TABLE_POINTS+4);
for (int i = 0; i < NUM_TABLE_POINTS+4; i++) { for (int i = 0; i < NUM_TABLE_POINTS+4; i++) {
double r = i*ewaldDX; double r = i*ewaldDX;
double alphaR = alphaEwald*r; double alphaR = alphaEwald*r;
ewaldScaleTable[i] = erfc(alphaR) + TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR); erfcTable[i] = erfc(alphaR);
ewaldScaleTable[i] = erfcTable[i] + TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR);
} }
} }
...@@ -473,14 +476,10 @@ void CpuNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& d ...@@ -473,14 +476,10 @@ void CpuNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& d
} }
float CpuNonbondedForce::erfcApprox(float x) { float CpuNonbondedForce::erfcApprox(float x) {
// This approximation for erfc is from Abramowitz and Stegun (1964) p. 299. They cite the following as float x1 = x*erfcDXInv;
// the original source: C. Hastings, Jr., Approximations for Digital Computers (1955). It has a maximum int index = min((int) floor(x1), NUM_TABLE_POINTS);
// error of 3e-7. float coeff2 = x1-index;
float coeff1 = 1.0f-coeff2;
float t = 1.0f+(0.0705230784f+(0.0422820123f+(0.0092705272f+(0.0001520143f+(0.0002765672f+0.0000430638f*x)*x)*x)*x)*x)*x; return coeff1*erfcTable[index] + coeff2*erfcTable[index+1];
t *= t;
t *= t;
t *= t;
return 1.0f/(t*t);
} }
platforms/cpu/src/CpuNonbondedForceVec4.cpp
View file @ bf6d95c2
/* Portions copyright (c) 2006-2014 Stanford University and Simbios. /* Portions copyright (c) 2006-2015 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -393,15 +393,16 @@ void CpuNonbondedForceVec4::getDeltaR(const fvec4& posI, const fvec4& x, const f ...@@ -393,15 +393,16 @@ void CpuNonbondedForceVec4::getDeltaR(const fvec4& posI, const fvec4& x, const f
} }
fvec4 CpuNonbondedForceVec4::erfcApprox(const fvec4& x) { fvec4 CpuNonbondedForceVec4::erfcApprox(const fvec4& x) {
// This approximation for erfc is from Abramowitz and Stegun (1964) p. 299. They cite the following as fvec4 x1 = x*erfcDXInv;
// the original source: C. Hastings, Jr., Approximations for Digital Computers (1955). It has a maximum ivec4 index = min(floor(x1), NUM_TABLE_POINTS);
// error of 3e-7. fvec4 coeff2 = x1-index;
fvec4 coeff1 = 1.0f-coeff2;
fvec4 t = 1.0f+(0.0705230784f+(0.0422820123f+(0.0092705272f+(0.0001520143f+(0.0002765672f+0.0000430638f*x)*x)*x)*x)*x)*x; fvec4 t1(&erfcTable[index[0]]);
t *= t; fvec4 t2(&erfcTable[index[1]]);
t *= t; fvec4 t3(&erfcTable[index[2]]);
t *= t; fvec4 t4(&erfcTable[index[3]]);
return 1.0f/(t*t); transpose(t1, t2, t3, t4);
return coeff1*t1 + coeff2*t2;
} }
fvec4 CpuNonbondedForceVec4::ewaldScaleFunction(const fvec4& x) { fvec4 CpuNonbondedForceVec4::ewaldScaleFunction(const fvec4& x) {
......
platforms/cpu/src/CpuNonbondedForceVec8.cpp
View file @ bf6d95c2
/* Portions copyright (c) 2006-2014 Stanford University and Simbios. /* Portions copyright (c) 2006-2015 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -423,15 +423,23 @@ void CpuNonbondedForceVec8::getDeltaR(const fvec4& posI, const fvec8& x, const f ...@@ -423,15 +423,23 @@ void CpuNonbondedForceVec8::getDeltaR(const fvec4& posI, const fvec8& x, const f
} }
fvec8 CpuNonbondedForceVec8::erfcApprox(const fvec8& x) { fvec8 CpuNonbondedForceVec8::erfcApprox(const fvec8& x) {
// This approximation for erfc is from Abramowitz and Stegun (1964) p. 299. They cite the following as fvec8 x1 = x*erfcDXInv;
// the original source: C. Hastings, Jr., Approximations for Digital Computers (1955). It has a maximum ivec8 index = min(floor(x1), NUM_TABLE_POINTS);
// error of 3e-7. fvec8 coeff2 = x1-index;
fvec8 coeff1 = 1.0f-coeff2;
fvec8 t = 1.0f+(0.0705230784f+(0.0422820123f+(0.0092705272f+(0.0001520143f+(0.0002765672f+0.0000430638f*x)*x)*x)*x)*x)*x; ivec4 indexLower = index.lowerVec();
t *= t; ivec4 indexUpper = index.upperVec();
t *= t; fvec4 t1(&erfcTable[indexLower[0]]);
t *= t; fvec4 t2(&erfcTable[indexLower[1]]);
return 1.0f/(t*t); fvec4 t3(&erfcTable[indexLower[2]]);
fvec4 t4(&erfcTable[indexLower[3]]);
fvec4 t5(&erfcTable[indexUpper[0]]);
fvec4 t6(&erfcTable[indexUpper[1]]);
fvec4 t7(&erfcTable[indexUpper[2]]);
fvec4 t8(&erfcTable[indexUpper[3]]);
fvec8 s1, s2, s3, s4;
transpose(t1, t2, t3, t4, t5, t6, t7, t8, s1, s2, s3, s4);
return coeff1*s1 + coeff2*s2;
} }
fvec8 CpuNonbondedForceVec8::ewaldScaleFunction(const fvec8& x) { fvec8 CpuNonbondedForceVec8::ewaldScaleFunction(const fvec8& x) {
......
platforms/cpu/src/gmx_atomic.h
View file @ bf6d95c2
...@@ -64,6 +64,7 @@ ...@@ -64,6 +64,7 @@
#include <stdio.h> #include <stdio.h>
#define NOMINMAX
#include <pthread.h> #include <pthread.h>
#ifdef __cplusplus #ifdef __cplusplus
......
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