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Commit 51475608 authored by Peter Eastman's avatar Peter Eastman
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Deleted lots of obsolete code

parent 398f0609
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platforms/reference/src/SimTKReference/ReferenceConstraint.h
View file @ 51475608
...@@ -137,11 +137,6 @@ class ReferenceShakeConstraint : public ReferenceConstraint { ...@@ -137,11 +137,6 @@ class ReferenceShakeConstraint : public ReferenceConstraint {
int getLightAtomIndex( void ); int getLightAtomIndex( void );
}; };
typedef std::vector<ReferenceShakeConstraint*> ShakeVector;
typedef ShakeVector::iterator ShakeVectorI;
typedef std::map<int, ShakeVector*> IntShakeMap;
typedef IntShakeMap::iterator IntShakeMapI;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
#endif // __ReferenceShakeConstraint_H__ #endif // __ReferenceShakeConstraint_H__
platforms/reference/src/SimTKUtilities/SimTKOpenMMCommon.cpp
View file @ 51475608
...@@ -36,15 +36,3 @@ const int SimTKOpenMMCommon::DefaultReturn = 0; ...@@ -36,15 +36,3 @@ const int SimTKOpenMMCommon::DefaultReturn = 0;
const int SimTKOpenMMCommon::ErrorReturn = -1; const int SimTKOpenMMCommon::ErrorReturn = -1;
const RealOpenMM SimTKOpenMMCommon::BigCutoffValue = 1.0e+05; const RealOpenMM SimTKOpenMMCommon::BigCutoffValue = 1.0e+05;
// units
const int SimTKOpenMMCommon::MdUnits = 1;
const int SimTKOpenMMCommon::KcalAngUnits = 2;
// specify RealOpenMM number format
const int SimTKOpenMMCommon::HighStringStreamNumberWidth = 20;
const int SimTKOpenMMCommon::HighStringStreamNumberPrecision = 12;
const RealOpenMM SimTKOpenMMCommon::DegreeToRadians = (RealOpenMM) 0.017453292;
platforms/reference/src/SimTKUtilities/SimTKOpenMMCommon.h
View file @ 51475608
...@@ -30,76 +30,18 @@ ...@@ -30,76 +30,18 @@
// STL includes // STL includes
#include <vector> #include <vector>
#include <map>
#include <set>
#include <string> #include <string>
// generic c includes
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#include <math.h>
#include <assert.h>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
#include "RealVec.h" #include "RealVec.h"
#include "SimTKOpenMMWindowLinux.h"
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
typedef std::vector<int> IntVector;
typedef IntVector::iterator IntVectorI;
typedef IntVector::const_iterator IntVectorCI;
typedef IntVector::reverse_iterator IntVectorRI;
typedef IntVector::const_reverse_iterator IntVectorCRI;
typedef std::map<int, int> IntIntMap;
typedef IntIntMap::iterator IntIntMapI;
typedef IntIntMap::const_iterator IntIntMapCI;
typedef std::set<int> IntSet;
typedef IntSet::iterator IntSetI;
typedef IntSet::const_iterator IntSetCI;
typedef std::vector<IntSet> IntSetVector;
typedef IntSetVector::iterator IntSetVectorI;
typedef IntSetVector::const_iterator IntSetVectorCI;
typedef std::multiset<int> IntMultiSet;
typedef IntMultiSet::iterator IntMultiSetI;
typedef IntMultiSet::const_iterator IntMultiSetCI;
typedef std::vector<std::string> StringVector;
typedef StringVector::iterator StringVectorI;
typedef StringVector::const_iterator StringVectorCI;
typedef std::map<std::string, std::string> StringStringMap;
typedef StringStringMap::iterator StringStringMapI;
typedef StringStringMap::const_iterator StringStringMapCI;
typedef std::vector<RealOpenMM> RealOpenMMVector; typedef std::vector<RealOpenMM> RealOpenMMVector;
typedef RealOpenMMVector::iterator RealOpenMMVectorI; typedef RealOpenMMVector::iterator RealOpenMMVectorI;
typedef RealOpenMMVector::const_iterator RealOpenMMVectorCI; typedef RealOpenMMVector::const_iterator RealOpenMMVectorCI;
typedef std::vector<RealOpenMM*> RealOpenMMPtrVector;
typedef RealOpenMMPtrVector::iterator RealOpenMMPtrVectorI;
typedef RealOpenMMPtrVector::const_iterator RealOpenMMPtrVectorCI;
typedef std::vector<RealOpenMM**> RealOpenMMPtrPtrVector;
typedef RealOpenMMPtrPtrVector::iterator RealOpenMMPtrPtrVectorI;
typedef RealOpenMMPtrPtrVector::const_iterator RealOpenMMPtrPtrVectorCI;
typedef std::map<std::string, RealOpenMM> StringRealOpenMMMap;
typedef StringRealOpenMMMap::iterator StringRealOpenMMMapI;
typedef StringRealOpenMMMap::const_iterator StringRealOpenMMMapCI;
typedef std::map<std::string, int> StringIntMap;
typedef StringIntMap::iterator StringIntMapI;
typedef StringIntMap::const_iterator StringIntMapCI;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
class SimTKOpenMMCommon { class SimTKOpenMMCommon {
...@@ -118,83 +60,6 @@ class SimTKOpenMMCommon { ...@@ -118,83 +60,6 @@ class SimTKOpenMMCommon {
static const int DefaultReturn; static const int DefaultReturn;
static const int ErrorReturn; static const int ErrorReturn;
// units
static const int MdUnits;
static const int KcalAngUnits;
// specify RealOpenMM number format
static const int HighStringStreamNumberWidth;
static const int HighStringStreamNumberPrecision;
static const RealOpenMM DegreeToRadians;
/**---------------------------------------------------------------------------------------
Get string w/ minimum desired width
@param inputString input string
@param desiredSize minimum desired size of output string
@param spacer string to append to inputString to get desired width (" ")
@return DefaultReturn
--------------------------------------------------------------------------------------- */
static std::string getSpacedString( const std::string&, int desiredSize = 25,
const std::string& spacer = " " );
}; };
// ---------------------------------------------------------------------------------------
// StringComparisonForMap: used to compare strings in STL maps w/ strings as keys
#ifndef StringComparisonForMapPtrBlcok
#define StringComparisonForMapPtrBlcok
// above define should be removed once CommonTk is removed
class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
public:
bool operator()( const std::string* str1, const std::string* str2 ) const {
return strcmp( str1->c_str(), str2->c_str() ) < 0;
}
};
class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
public:
bool operator()( const std::string& str1, const std::string& str2 ) const {
return strcmp( str1.c_str(), str2.c_str() ) < 0;
}
};
#endif
// ---------------------------------------------------------------------------------------
// Used to compare integers for sorting, ...
int numericCompareI( const void* point1, const void* point2 );
// ---------------------------------------------------------------------------------------
// string-string map and iterator definitions
typedef std::map<std::string, std::string, StringComparisonForMap> StringMap;
typedef StringMap::iterator StringMapI;
typedef StringMap::const_iterator StringMapCI;
// string set and iterator definitions
typedef std::set<std::string, StringComparisonForMap> StringSet;
typedef StringSet::iterator StringSetI;
typedef StringSet::const_iterator StringSetCI;
// ---------------------------------------------------------------------------------------
#endif // __SimTKOpenMMCommon_H__ #endif // __SimTKOpenMMCommon_H__
platforms/reference/src/SimTKUtilities/SimTKOpenMMGpuUtilities.h deleted 100755 → 0
View file @ 398f0609
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __SimTKOpenMMGpuUtilities_H_
#define __SimTKOpenMMGpuUtilities_H_
// ---------------------------------------------------------------------------------------
// reserve the option to change between Real and double
#include "SimTKOpenMMRealType.h"
#include "SimTKOpenMMCommon.h"
// ---------------------------------------------------------------------------------------
// class of shared, static utility methods
#include <stdio.h>
#include <string.h>
#include <string>
#include <stdlib.h>
#include <sstream>
// #include <string>
// ---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
Class of static methods to be shared
Most methods are standalone 'utility' methods
--------------------------------------------------------------------------------------- */
class SimTKOpenMMGpuUtilities {
public:
// dummy constructor/destructor
SimTKOpenMMGpuUtilities(){};
~SimTKOpenMMGpuUtilities(){};
/**---------------------------------------------------------------------------------------
Helper method to repack RealOpenMM arrays (Simbios)
@param numberOfEntries entries/sub-array
@param subarraySize number of subarrays
@param array array
Input array = [subArray_1 subArray_2 subArray_3 ... subArray_Stacked] \n
where each subArray_i is 1 x numberOfEntries
Output array = [ subArray_1_1 subArray_2_1 subArray_3_1 ... subArray_Stacked_1 \n
subArray_1_2 subArray_2_2 subArray_3_2 ... subArray_Stacked_2 \n
subArray_1_3 subArray_2_3 subArray_3_3 ... subArray_Stacked_3 \n
... \n
subArray_1_N subArray_2_N subArray_3_N ... subArray_Stacked_N ] \n
where N = numberOfEntries
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int repackArray1( int numberOfEntries, int subarraySize, RealOpenMM* array );
/**---------------------------------------------------------------------------------------
Copy an array into a packed (e.g., RealOpenMM4 array) (Simbios)
Example copy Born radii into last slot of force array
@param numberOfEntries entries/sub-array (no. atoms)
@param subarraySize number of subarrays (4 for RealOpenMM4)
@param fullArray full array (force array in example)
@param copySlot index of slot to copied into (3 in example, since want Born radius in .w slot)
@param arrayToCopy array to copy (Born array)
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int copySubArray( int numberOfEntries, int subarraySize, RealOpenMM* fullArray,
int copySlot, RealOpenMM* arrayToCopy );
/**---------------------------------------------------------------------------------------
Helper method to repack RealOpenMM arrays (Simbios)
@param numberOfEntries entries/sub-array
@param subarraySize number of subarrays
@param array array
Input array = [subArray_1 subArray_2 subArray_3 ... subArray_N] \n
where each subArray_i is vector of length M=numberOfEntries \n
Output array = [ subArray_1_1 subArray_2_1 subArray_3_1 ... subArray_N_1 \n
subArray_1_2 subArray_2_2 subArray_3_2 ... subArray_N_2 \n
subArray_1_3 subArray_2_3 subArray_3_3 ... subArray_N_3 \n
... \n
subArray_1_M subArray_2_M subArray_3_M ... subArray_M ] \n
where N = numberOfEntries \n
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int repackArray( int numberOfEntries, int subarraySize, RealOpenMM* array );
/**---------------------------------------------------------------------------------------
Helper method to repack RealOpenMM arrays (Simbios)
@param numberOfEntries entries/sub-array
@param subarraySize number of subarrays
@param array repacked output array
@param inputArrays inputArrays[subarraySize][numberOfEntries]
Output array = [ inputArrays[0][0] inputArrays[1][0] inputArrays[2][0] inputArrays[3][0] \n
inputArrays[0][1] inputArrays[1][1] inputArrays[2][1] inputArrays[3][1] \n
inputArrays[0][2] inputArrays[1][2] inputArrays[2][2] inputArrays[3][2] \n
... \n
inputArrays[0][numberOfEntries] ... inputArrays[subarraySize-1][numberOfEntries] \n
] \n
where N = numberOfEntries \n
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int repackArrayOfArrays( int numberOfEntries, int subarraySize,
RealOpenMM* array, RealOpenMM** inputArrays );
/**---------------------------------------------------------------------------------------
Collapse 2D array into packed single array (Simbios)
Example forces[3][N] -> array of size N containing RealOpenMM3 values
@param numberOfEntries entries (no. atoms)
@param iUnroll iUnroll
@param jUnroll jUnroll
@param arrays arrays to be merged (dimension is [iUnroll][numberOfEntries/iUnroll]
@param mergeArray output array (if null, then allocated)
@param log logging file descriptor
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static RealOpenMM* collapseArrays( int numberOfEntries, int iUnroll, int jUnroll,
RealOpenMM** arrays, RealOpenMM* mergeArray, FILE* log );
/**---------------------------------------------------------------------------------------
Merge 2 arrays based on sentinel value (Simbios)
Overflow array, if present, signals which entries had nonsentinel in both arrays
Example \n
array1 = { 1, 2, 3, s, s, s, 4, 5, s } \n
array2 = { s, s, 6, 8, 9, 3, s, 7, s } \n
merge array = { 1, 2, 3, 8, 9, 3, 4, 5, s } \n
overflow array = { s, s, 6, s, s, s, s, 7, s } \n
@param numberOfEntries entries (no. atoms)
@param sentinelValue sentinel value
@param array1 first array
@param array2 second array
@param mergeArray output merge array
@param overflowArray output overflow array (if null, then ignored)
@param log logging file descriptor
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int mergeArraysBasedSentinelValue( int numberOfEntries,
RealOpenMM sentinelValue,
RealOpenMM* array1, RealOpenMM* array2,
RealOpenMM* mergeArray, RealOpenMM* overflowArray,
FILE* log );
/**---------------------------------------------------------------------------------------
Helper method to store values from CPU loop in position seen in GPU output (Simbios)
--------------------------------------------------------------------------------------- */
static int storeInGpuFormat( int atomI, int atomJ, int debugAtomJ,
int jUnroll, int numberOfStreams,
RealOpenMM** debugStreams, RealOpenMM* RealOpenMMValues[2],
RealOpenMM unsetDebugValue, bool useUpper, FILE* log );
/**---------------------------------------------------------------------------------------
Helper method to compare cpu and gpu computed arrays
@param numberOfAtoms entries (no. atoms)
@param chunkSize chunk size (usually 3 or 4)
@param cpuArray cpuArray[0-(chunkSize-1)][0,entries-1]
@param gpuArray gpuArray[chunkSize*entries]
@param tolerance check if relative difference is greater
than this tolerance
@param compareColumn array of size [chunkSize] signalling whether
column i is to be compared; it may be NULL
@param absoluteMin error if abs(cpu) + abs(gpu) > absoluteMin
set negative to ignore this condition
@param printOn if not set, then no printing
@param header id header -- optional
@param log logging file descriptor
@return number of failed entries
--------------------------------------------------------------------------------------- */
static int compareCpuGpuArrays( int numberOfAtoms, int chunkSize,
RealOpenMM** cpuArray, RealOpenMM* gpuArray,
RealOpenMM tolerance,
int* compareColumn, RealOpenMM absoluteMin,
int printOn, const char* header, FILE* log );
// ---------------------------------------------------------------------------------------
};
// ---------------------------------------------------------------------------------------
#endif // __SimTKOpenMMGpuUtilities_H__
platforms/reference/src/SimTKUtilities/SimTKOpenMMLog.h
View file @ 51475608
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __SimTKOpenMMLog_H__ #ifndef __SimTKOpenMMLog_H__
#define __SimTKOpenMMLog_H__ #define __SimTKOpenMMLog_H__
#include <stdio.h> #include <cstdio>
#include <sstream> #include <sstream>
#include "SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "openmm/internal/windowsExport.h" #include "openmm/internal/windowsExport.h"
......
platforms/reference/src/SimTKUtilities/SimTKOpenMMRealType.h
View file @ 51475608
...@@ -26,7 +26,7 @@ ...@@ -26,7 +26,7 @@
#ifndef __RealSimTk_H__ #ifndef __RealSimTk_H__
#define __RealSimTk_H__ #define __RealSimTk_H__
#include <math.h> #include <cmath>
// Set RealOpenMMType to 2 for double precision, 1 for float // Set RealOpenMMType to 2 for double precision, 1 for float
......
platforms/reference/src/SimTKUtilities/SimTKOpenMMUtilities.h
View file @ 51475608
...@@ -31,19 +31,7 @@ ...@@ -31,19 +31,7 @@
#include "sfmt/SFMT.h" #include "sfmt/SFMT.h"
#include "openmm/internal/windowsExport.h" #include "openmm/internal/windowsExport.h"
#include <stdio.h>
#include <string.h>
#include <string> #include <string>
#include <stdlib.h>
#include <sstream>
// template is used to check if a string is integer, real, ...
template <class T>
bool checkString( T& t, const std::string& s, std::ios_base& (*f)(std::ios_base&) ){
std::istringstream iss(s);
return !(iss >> f >> t).fail();
}
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -64,10 +52,6 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -64,10 +52,6 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
public: public:
// file flag enums
enum FileFlags { OpenDebugFile, WriteDebugFile, CloseDebugFile };
// dummy constructor/destructor // dummy constructor/destructor
SimTKOpenMMUtilities(){}; SimTKOpenMMUtilities(){};
...@@ -110,95 +94,6 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -110,95 +94,6 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
static int getDistanceSquaredFromSpecifiedPoint( RealOpenMM** atomCoordinates, RealOpenMM* point, static int getDistanceSquaredFromSpecifiedPoint( RealOpenMM** atomCoordinates, RealOpenMM* point,
int numberOfAtoms, RealOpenMM* distances, int numberOfAtoms, RealOpenMM* distances,
FILE* log ); FILE* log );
/**---------------------------------------------------------------------------------------
Helper method to allocate RealOpenMM arrays (Simbios)
@param bufferIndex buffer index
@param allocatedSz array of allocated sizes
@param bufferArray array of allocated RealOpenMM arrays
@param requestedSize requested size
@param dataAction action flag: -1 = free memory \n
1 = zero memory
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int allocateRealOpenMMBufferArray( int bufferIndex, int* allocatedSz,
RealOpenMM** bufferArray,
int requestedSize, int dataAction );
/**---------------------------------------------------------------------------------------
Print atom coordinates, ...
@param numberAtoms numberAtoms
@param atomCoordinates atomCoordinates (may be NULL)
@param numberOf1Darrays number of 1-d arrays (may be 0)
@param oneDArrays 1-d arrays
@param idString id string to be printed if set
@param log print messages to log file
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int printCoordinateAnd1DArrays( int numberAtoms, RealOpenMM** atomCoordinates,
int numberOf1Darrays, RealOpenMM** oneDArrays,
const char* idString, FILE* log );
/**---------------------------------------------------------------------------------------
Free array of strings
@param arraySz atom index
@param arrayOfStrings array of strings
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int freeArrayOfStrings( int arraySz, char** arrayOfStrings );
/**---------------------------------------------------------------------------------------
Tab string in place
@param string string to tab; assume string is of at least length=tab + 1
@param tab tab length
--------------------------------------------------------------------------------------- */
static int tabStringInPlace( char* string, int tab );
/**---------------------------------------------------------------------------------------
Write debug fields (Simbios)
@param numberOfFields number of fields to print
@param fields fields
@param numberOfStringFields number of string fields to print
@param stringFields string fields
@param comment comment (optinal -- ignored if NULL)
@param debugFileName output debug file name
@param action 0 open file and @return w/o printing
1 open file and print
2 close file (no print)
@param debugFile debug file reference
@param log if set, then print error messages to log file
@return debugFile unless file is closed
stringFields printed after RealOpenMM fields
--------------------------------------------------------------------------------------- */
static FILE* writeDebugFile( int numberOfFields, const RealOpenMM* fields,
int numberOfStringFields, const StringVector& stringFields,
const char* comment, const char* debugFileName, int action,
FILE* debugFile, FILE* log );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -292,40 +187,6 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -292,40 +187,6 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
static int initialize2DRealOpenMMArray( int iSize, int jSize, static int initialize2DRealOpenMMArray( int iSize, int jSize,
RealOpenMM** array2D, RealOpenMM initialValue ); RealOpenMM** array2D, RealOpenMM initialValue );
/**---------------------------------------------------------------------------------------
Malloc memory of size bytesToAllocate and zero
@param bytesToAllocate bytes to allocate
@return ptr to allocated memory; NULL if bytesToAllocate <= 0
--------------------------------------------------------------------------------------- */
static char* allocateAndZero( unsigned int bytesToAllocate );
/**---------------------------------------------------------------------------------------
Normalize 3-vector -- helper method
@param vector vector to normalize
--------------------------------------------------------------------------------------- */
static void normalizeVector3( RealOpenMM* vector );
/**---------------------------------------------------------------------------------------
Remove 3-vector -- helper method
@param vectorToRemove vector to remove
@param vector vector to from which 'vectorToRemove' is to be removed \n
vector is normalized after the component is subtracted out
--------------------------------------------------------------------------------------- */
static void removeVector3( RealOpenMM* vectorToRemove, RealOpenMM* vector );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Compute cross product of two 3-vectors and place in 3rd vector -- helper method Compute cross product of two 3-vectors and place in 3rd vector -- helper method
...@@ -341,250 +202,6 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -341,250 +202,6 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void crossProductVector3( RealOpenMM* vectorX, RealOpenMM* vectorY, RealOpenMM* vectorZ ); static void crossProductVector3( RealOpenMM* vectorX, RealOpenMM* vectorY, RealOpenMM* vectorZ );
/**---------------------------------------------------------------------------------------
Compute matrix product of 3x3 matrix and 3-vector and place in 3rd vector -- helper method
@param vectorZ = matrixX . vectorY
@param matrixX matrixX
@param vectorY y-vector
@param vectorZ z-vector
@return vector is vectorZ
--------------------------------------------------------------------------------------- */
static void matrixProductVector3( RealOpenMM* matrixX, RealOpenMM* vectorY, RealOpenMM* vectorZ );
/**---------------------------------------------------------------------------------------
Compute cross product between two 3x3 matrices
@param vectorZ = matrixX . matrixY
@param matrixX matrixX
@param matrixY matrixY
@param vectorZ z-vector
@return vector is vectorZ
--------------------------------------------------------------------------------------- */
static void matrixCrossProductMatrix3( RealOpenMM* matrixX, RealOpenMM* matrixY, RealOpenMM* vectorZ );
/* ---------------------------------------------------------------------------------------
Centralized malloc/new
@param name ptr name
@param fileName file name
@param line file line no.
@param file line size in bytes to be allocated
@return ptr to allocated object
--------------------------------------------------------------------------------------- */
static void* Xmalloc( const char* name, const char* fileName, int line, unsigned int size );
/* ---------------------------------------------------------------------------------------
Centralized free/delete
@param name ptr name
@param fileName file name
@param line file line no.
@param ptr ptr to be freed
--------------------------------------------------------------------------------------- */
static void Xfree( const char* name, const char* fileName, int line, void* ptr );
/* ---------------------------------------------------------------------------------------
Format array of reals
@param message input string stream
@param realArray array of RealOpenMMs
@param numberOfFields number of fields (optional - defaults to 3)
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int formatRealStringStream( std::stringstream& message, const RealOpenMM* realArray,
int numberOfFields = 3, RealOpenMM factor = (RealOpenMM) 1.0f );
/**---------------------------------------------------------------------------------------
Tokenize a string (static method) (Simbios)
@param lineBuffer string to tokenize
@param tokenArray upon return vectory of tokens
@param delimiter token delimter
@return number of args
--------------------------------------------------------------------------------------- */
static int tokenizeString( char* lineBuffer, StringVector& tokenArray, const std::string delimiter = "\t\n " );
/**---------------------------------------------------------------------------------------
Tokenize a string (static method) (Simbios)
@param line string to tokenize
@param tokenVector upon return vector of tokens
@param delimiter token delimter
@param clearTokenVector if true, clear tokenVector
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int tokenizeString( const std::string& line, StringVector& tokenVector,
const std::string& delimiter, int clearTokenVector );
/**---------------------------------------------------------------------------------------
Local version of strncasecmp (missing in Windows) (static method) (Simbios)
@param string1 first string
@param string2 second string
@param matchLength match length
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int localStrncasecmp( const char *string1, const char *string2, int matchLength );
/**---------------------------------------------------------------------------------------
Check that string is valid integer
@param stringToCheck string to check
@return true if string is a valid integer
--------------------------------------------------------------------------------------- */
static bool isValidInteger( std::string stringToCheck );
/**---------------------------------------------------------------------------------------
Check that string is valid RealOpenMM
@param stringToCheck string to check
@return true if string is a valid RealOpenMM
--------------------------------------------------------------------------------------- */
static bool isValidRealOpenMM( std::string stringToCheck );
/**---------------------------------------------------------------------------------------
Read file into string vector (Simbios)
@param fileName file name
@param fileContents string vector containing file contents upon return
one string per line
@return SimTKOpenMMCommon::DefaultReturn unless file could not be opened
--------------------------------------------------------------------------------------- */
static int readFileIntoStringVector( const std::string& fileName, StringVector& fileContents );
/**---------------------------------------------------------------------------------------
Read file into string vector (Simbios)
@param charArray character array
@param arrayLength array length
@param arrayContents string vector containing array contents upon return
one string per line
@return SimTKOpenMMCommon::DefaultReturn unless file could not be opened
--------------------------------------------------------------------------------------- */
static int readCharacterArrayIntoStringVector( const char* charArray, int arrayLength,
StringVector& fileContents );
/**---------------------------------------------------------------------------------------
Replacement of sorts for strtok() (static method) (Simbios)
Used to parse parameter file lines
Should be moved to Utilities file
@param lineBuffer string to tokenize
@param delimiter token delimter
@return number of args; if return value equals maxTokens, then more tokens than allocated
--------------------------------------------------------------------------------------- */
static char* strsep( char** lineBuffer, const char* delimiter );
/**---------------------------------------------------------------------------------------
Write file (helper method) (Simbios)
@param lineVector line entries for file
@param inputFileName inputFileName
@return SimTKOpenMMCommon::ErrorReturn if error -- else SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int writeFile( const StringVector& lineVector, const std::string& fileName );
/**---------------------------------------------------------------------------------------
Get statistics on an array
@param numberOfEntries number of entries in array
@param array array
@param average average of array on output
@param stdDev std dev of array on output
@param minValue min value in array on output
@param minIndex index of min value in array on output
@param maxValue max value in array on output
@param maxIndex index of max value in array on output
if numberOfEntries <= 0, return 0 for all RealOpenMM values and -1 for index values
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int getArrayStatistics( int numberOfEntries, const RealOpenMM* array,
RealOpenMM* average, RealOpenMM* stdDev,
RealOpenMM* minValue, int* minIndex,
RealOpenMM* maxValue, int* maxIndex );
/**---------------------------------------------------------------------------------------
Get one 2D array to another
@param dimension1 first dimension
@param dimension2 second dimension
@param arrayToAdd array to add [dimension1][dimension2]
@param sumArray summed array to add [dimension1][dimension2]
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int addTwoDimArray( int dimension1, int dimension2, RealOpenMM** arrayToAdd,
RealOpenMM** sumArray );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKUtilities/SimTKOpenMMWindowLinux.h deleted 100755 → 0
View file @ 398f0609
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __SimTKOpenMMWindowLinux_H_
#define __SimTKOpenMMWindowLinux_H__
#ifdef WIN32
#define FOPEN fopen_s
#else
#define FOPEN fopen
#endif
#endif // __SimTKOpenMMWindowLinux_H__
platforms/reference/src/SimTKUtilities/SimTKlapack.h deleted 100755 → 0
View file @ 398f0609
This diff is collapsed.
platforms/reference/src/SimTKUtilities/TwoDimArraySimTk.h deleted 100755 → 0
View file @ 398f0609
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __TwoDimArraySimTk_H_
#define __TwoDimArraySimTk_H_
// ---------------------------------------------------------------------------------------
//#include "SimTKOpenMMUtilities.h"
#include "SimTKOpenMMUtilities.h"
/**---------------------------------------------------------------------------------------
Class for 2D arrays
--------------------------------------------------------------------------------------- */
template <typename T> class TwoDimArraySimTk {
private:
int _rowSize;
int _columnSize;
T** _2Darray;
T* _2DMemoryBlock;
std::string _name;
public:
TwoDimArraySimTk( int rowSize, int columnSize );
~TwoDimArraySimTk();
/**---------------------------------------------------------------------------------------
Get 2D array
@return ptr to array
--------------------------------------------------------------------------------------- */
T** get2DArray( void ) const { return _2Darray; };
/**---------------------------------------------------------------------------------------
Get print string
@return std::string
--------------------------------------------------------------------------------------- */
std::string getPrintString( void ) const;
/**---------------------------------------------------------------------------------------
Get name
@return array name
--------------------------------------------------------------------------------------- */
std::string getName( void ) const { return _name; };
/**---------------------------------------------------------------------------------------
Set name
@param array name
--------------------------------------------------------------------------------------- */
void setName( std::string name ){ _name = name; };
};
/**---------------------------------------------------------------------------------------
TwoDimArraySimTk constructor
@param rowSize row dimension
@param columnSize column dimension
--------------------------------------------------------------------------------------- */
template <typename T>
TwoDimArraySimTk<T>::TwoDimArraySimTk( int rowSize, int columnSize ){
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nTwoDimArraySimTk<T>::TwoDimArraySimTk";
// ---------------------------------------------------------------------------------------
_name = "NotSet";
_rowSize = rowSize;
_columnSize = columnSize;
#ifdef useXMalloc
_2Darray = (T**) SimTKOpenMMUtilities::Xmalloc( "TwoDimArraySimTk", __FILE__, __LINE__, rowSize*sizeof( T* ) );
_2DMemoryBlock = (T*) SimTKOpenMMUtilities::Xmalloc( "block", __FILE__, __LINE__, columnSize*rowSize*sizeof( T ) );
#else
_2Darray = (T**) SimTKOpenMMUtilities::Xmalloc( "TwoDimArraySimTk", __FILE__, __LINE__, rowSize*sizeof( T* ) );
_2DMemoryBlock = (T*) SimTKOpenMMUtilities::Xmalloc( "block", __FILE__, __LINE__, columnSize*rowSize*sizeof( T ) );
#endif
T* blockPtr = _2DMemoryBlock;
for( int ii = 0; ii < rowSize; ii++ ){
_2Darray[ii] = blockPtr;
blockPtr += columnSize;
}
memset( _2DMemoryBlock, 0, columnSize*rowSize*sizeof( T ) );
// (void) fprintf( stdout, "\nTwoDimArraySimTk %s ", getPrintString().c_str() );
// (void) fflush( stdout );
}
/**---------------------------------------------------------------------------------------
TwoDimArraySimTk destructor
array[i][j]
@param rowSize row dimension
@param columnSize column dimension
--------------------------------------------------------------------------------------- */
template <typename T> TwoDimArraySimTk<T>::~TwoDimArraySimTk( ){
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nTwoDimArraySimTk<T>::~TwoDimArraySimTk";
// ---------------------------------------------------------------------------------------
if( _2DMemoryBlock ){
SimTKOpenMMUtilities::Xfree( "2DMemoryBlock", __FILE__, __LINE__, _2DMemoryBlock );
}
if( _2Darray ){
SimTKOpenMMUtilities::Xfree( "2Darray", __FILE__, __LINE__, _2Darray );
}
}
/**---------------------------------------------------------------------------------------
TwoDimArraySimTk print string
@return id string
--------------------------------------------------------------------------------------- */
template <typename T> std::string TwoDimArraySimTk<T>::getPrintString( void ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nTwoDimArraySimTk<T>::getPrintString";
// ---------------------------------------------------------------------------------------
std::stringstream message;
message << _name << " [ " << _rowSize << ", " << _columnSize << " ] sizeT=" << sizeof( T );
message << " array=" << (unsigned int) _2Darray << " block=" << (unsigned int) _2DMemoryBlock;
// message << " array=" << (void *) _2Darray << " block=" << (void*) _2DMemoryBlock;
return message.str();
}
/**---------------------------------------------------------------------------------------
Typdefs to make code more readable
--------------------------------------------------------------------------------------- */
typedef TwoDimArraySimTk<Real> TwoDimRealArraySimTk;
typedef std::vector<TwoDimRealArraySimTk*> TwoDimRealArraySimTkVector;
typedef std::vector<TwoDimRealArraySimTk*>::iterator TwoDimRealArraySimTkVectorI;
#endif // __TwoDimArraySimTk_H_
platforms/reference/src/gbsa/CpuImplicitSolvent.cpp
View file @ 51475608
...@@ -42,19 +42,6 @@ using namespace std; ...@@ -42,19 +42,6 @@ using namespace std;
CpuImplicitSolvent* CpuImplicitSolvent::_cpuImplicitSolvent = NULL; CpuImplicitSolvent* CpuImplicitSolvent::_cpuImplicitSolvent = NULL;
// info file related-stuff
std::string CpuImplicitSolvent::_defaultInfoFileName = std::string( "CpuImplicitSolventInfo" );
// key for info file: base file name
const std::string CpuImplicitSolvent::CpuImplicitSolventBaseFileName = std::string( "CpuImplicitSolventBaseFileName" );
// key for info file: file generation frequency
const std::string CpuImplicitSolvent::CpuImplicitSolventFileGenerationFrequency = std::string( "CpuImplicitSolventFileGenerationFrequency" );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
CpuImplicitSolvent constructor CpuImplicitSolvent constructor
...@@ -115,9 +102,6 @@ void CpuImplicitSolvent::_initializeDataMembers( void ){ ...@@ -115,9 +102,6 @@ void CpuImplicitSolvent::_initializeDataMembers( void ){
_forceCallIndex = 0; _forceCallIndex = 0;
_implicitSolventEnergy = (RealOpenMM) 0.0; _implicitSolventEnergy = (RealOpenMM) 0.0;
_baseFileName = SimTKOpenMMCommon::NotSet;
_outputFileFrequency = 1;
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -740,243 +724,6 @@ int CpuImplicitSolvent::computeAceNonPolarForce( const ImplicitSolventParameters ...@@ -740,243 +724,6 @@ int CpuImplicitSolvent::computeAceNonPolarForce( const ImplicitSolventParameters
} }
/**---------------------------------------------------------------------------------------
Get BaseFileName
@return baseFileName
--------------------------------------------------------------------------------------- */
const std::string& CpuImplicitSolvent::getBaseFileName( void ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nCpuImplicitSolvent::getBaseFileName";
// ---------------------------------------------------------------------------------------
return _baseFileName;
}
/**---------------------------------------------------------------------------------------
Set BaseFileName
@param input baseFileName
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int CpuImplicitSolvent::setBaseFileName( const std::string& baseFileName ){
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nCpuImplicitSolvent::setBaseFileName";
// ---------------------------------------------------------------------------------------
_baseFileName = baseFileName;
return SimTKOpenMMCommon::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Set OutputFileFrequency
@param input outputFileFrequency
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int CpuImplicitSolvent::setOutputFileFrequency( int outputFileFrequency ){
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nCpuImplicitSolvent::setOutputFileFrequency";
// ---------------------------------------------------------------------------------------
_outputFileFrequency = outputFileFrequency;
return SimTKOpenMMCommon::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Get OutputFileFrequency
@return output file frequency
--------------------------------------------------------------------------------------- */
int CpuImplicitSolvent::getOutputFileFrequency( void ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nCpuImplicitSolvent::getOutputFileFrequency";
// ---------------------------------------------------------------------------------------
return _outputFileFrequency;
}
/**---------------------------------------------------------------------------------------
Read info file
@param infoFileName file name to read
@return SimTKOpenMMCommon::DefaultReturn if ok; else SimTKOpenMMCommon::ErrorReturn; if major
problem, program will exit
--------------------------------------------------------------------------------------- */
int CpuImplicitSolvent::readInfoFile( const std::string infoFileName ){
// ---------------------------------------------------------------------------------------
const int bufferSize = 2048;
char buffer[bufferSize];
static const std::string methodName = "\nCpuImplicitSolvent::readInfoFile";
// ---------------------------------------------------------------------------------------
FILE* infoFile = NULL;
#ifdef _MSC_VER
fopen_s( &infoFile, infoFileName.c_str(), "r" );
#else
infoFile = fopen( infoFileName.c_str(), "r" );
#endif
if( infoFile == NULL ){
#ifdef _MSC_VER
fopen_s( &infoFile, _defaultInfoFileName.c_str(), "r" );
#else
infoFile = fopen( _defaultInfoFileName.c_str(), "r" );
#endif
if( infoFile == NULL ){
std::stringstream message;
message << methodName << " fopen failed on info file=<" << _defaultInfoFileName << "> and file=<" << infoFileName << ">";
SimTKOpenMMLog::printMessage( message );
return SimTKOpenMMCommon::ErrorReturn;
} else {
std::stringstream message;
message << methodName << " opened info file=<" << _defaultInfoFileName << ">.";
SimTKOpenMMLog::printMessage( message );
}
} else {
std::stringstream message;
message << methodName << " opened info file=<" << infoFileName << ">.";
SimTKOpenMMLog::printMessage( message );
}
/* Sample file:
*/
int errors = 0;
while( fgets( buffer, bufferSize, infoFile ) ){
std::stringstream message;
std::string fileName = std::string( );
size_t bufferLen = strlen( buffer );
if( bufferLen > 0 ){
buffer[bufferLen-1] = '\0';
}
message << "\n<" << buffer << ">";
//fprintf( amoebaLog->getLogFile(), "\nreadInfoFile <%s>", buffer );
//fflush( amoebaLog->getLogFile() );
StringVector tokens;
SimTKOpenMMUtilities::tokenizeString( buffer, tokens );
bool done = false;
for( StringVectorI ii = tokens.begin(); ii != tokens.end() && !done; ii++ ){
std::string token = *ii;
size_t tokenLength = token.length();
bool recognized = false;
// skip comments and blank lines
if( tokenLength < 2 || !token.compare( "#" ) ){
done = true;
recognized = true;
// base file name
} else if( !token.compare( CpuImplicitSolvent::CpuImplicitSolventBaseFileName ) ){
recognized = true;
setBaseFileName( *(++ii) );
// file frequency
} else if( !token.compare( CpuImplicitSolvent::CpuImplicitSolventFileGenerationFrequency ) ){
recognized = true;
std::string value = *(++ii);
if( SimTKOpenMMUtilities::isValidInteger( value ) ){
setOutputFileFrequency( atoi( value.c_str() ) );
} else {
message << "\nToken=<" << token << "> is not a valid integer for key=" << CpuImplicitSolvent::CpuImplicitSolventFileGenerationFrequency;
}
// keys used by objects other than 'CpuImplicitSolvent'
} else {
/*
recognized = true;
std::string key = *ii;
ii++;
if( ii != tokens.end() ){
_inputArguments[key] = *ii;
} else {
_inputArguments[key] = CpuImplicitSolventCommon::Comment;
}
*/
}
if( !recognized ){
message << "\nToken=<" << token << "> not recognized.";
}
}
SimTKOpenMMLog::printMessage( message );
}
(void) fclose( infoFile );
// report if errors
if( errors ){
std::stringstream message;
message << "\nErrors -- aborting.\n";
SimTKOpenMMLog::printMessage( message );
exit(-1);
} else {
std::stringstream message;
message << "\nNo errors detected parsing info file " << infoFileName << "\n";
/*
message << "\nNumber of hash arguments=" << _amoebaInputArguments.size() << " <key,value> pairs listed below:\n";
for( StringStringMapCI ii = _amoebaInputArguments.begin(); ii != _amoebaInputArguments.end(); ii++ ){
message << "\n <" << (*ii).first << ">=<" << (*ii).second << ">";
}
*/
message << "\n\n";
SimTKOpenMMLog::printMessage( message );
}
return SimTKOpenMMCommon::DefaultReturn;
}
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Get string w/ state Get string w/ state
...@@ -1014,80 +761,3 @@ std::string CpuImplicitSolvent::getStateString( const char* title ) const { ...@@ -1014,80 +761,3 @@ std::string CpuImplicitSolvent::getStateString( const char* title ) const {
return message.str(); return message.str();
} }
/* ---------------------------------------------------------------------------------------
Override C++ new w/ Gromac's smalloc/sfree (Simbios)
@param size bytes to allocate
@return ptr to allocated memory
--------------------------------------------------------------------------------------- */
/*
void* CpuImplicitSolvent::operator new( size_t size ){
void *ptr;
smalloc(ptr, (int) size);
// (void) fprintf( stdout, "\nCpuImplicitSolvent new called -- size=%u", size );
// (void) fflush( stdout );
return ptr;
} */
/* ---------------------------------------------------------------------------------------
Override C++ delete w/ Gromac's sfree (Simbios)
@param ptr ptr to block to free
--------------------------------------------------------------------------------------- */
/*
void CpuImplicitSolvent::operator delete( void *ptr ){
// (void) fprintf( stdout, "\nCpuImplicitSolvent delete called." );
// (void) fflush( stdout );
sfree( ptr );
} */
/* ---------------------------------------------------------------------------------------
Override C++ new w/ Gromac's smalloc/sfree (Simbios)
@param size bytes to allocate
@return ptr to allocated memory
--------------------------------------------------------------------------------------- */
/*
void* CpuImplicitSolvent::operator new[]( size_t size ){
void *ptr;
smalloc(ptr, (int) size);
// (void) fprintf( stdout, "\nCpuImplicitSolvent new[] called -- size=%u", size );
// (void) fflush( stdout );
return ptr;
} */
/* ---------------------------------------------------------------------------------------
Override C++ delete w/ Gromac's sfree (Simbios)
@param ptr ptr to block to free
--------------------------------------------------------------------------------------- */
/*
void CpuImplicitSolvent::operator delete[]( void *ptr ){
// (void) fprintf( stdout, "\nCpuImplicitSolvent delete[] called." );
// (void) fflush( stdout );
sfree( ptr );
}
*/
platforms/reference/src/gbsa/CpuImplicitSolvent.h
View file @ 51475608
...@@ -32,27 +32,8 @@ ...@@ -32,27 +32,8 @@
class OPENMM_EXPORT CpuImplicitSolvent { class OPENMM_EXPORT CpuImplicitSolvent {
public:
// fields in info file
const static std::string CpuImplicitSolventBaseFileName;
const static std::string CpuImplicitSolventFileGenerationFrequency;
private: private:
// default info file name
static std::string _defaultInfoFileName;
// base file name
std::string _baseFileName;
// frequency to output diagnostic files
int _outputFileFrequency;
// used for direct calls // used for direct calls
static CpuImplicitSolvent* _cpuImplicitSolvent; static CpuImplicitSolvent* _cpuImplicitSolvent;
...@@ -155,14 +136,6 @@ class OPENMM_EXPORT CpuImplicitSolvent { ...@@ -155,14 +136,6 @@ class OPENMM_EXPORT CpuImplicitSolvent {
virtual ~CpuImplicitSolvent( ); virtual ~CpuImplicitSolvent( );
// override of new/delete -- used when run in PS3 framework(?)
// static void* operator new( size_t size );
// static void operator delete( void *p );
// static void* operator new[]( size_t size );
// static void operator delete[]( void *p );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Delete static _cpuImplicitSolvent object if set Delete static _cpuImplicitSolvent object if set
...@@ -419,112 +392,6 @@ class OPENMM_EXPORT CpuImplicitSolvent { ...@@ -419,112 +392,6 @@ class OPENMM_EXPORT CpuImplicitSolvent {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
std::string getStateString( const char* title ) const; std::string getStateString( const char* title ) const;
/**---------------------------------------------------------------------------------------
Get BaseFileName
@return baseFileName
--------------------------------------------------------------------------------------- */
const std::string& getBaseFileName( void ) const;
/**---------------------------------------------------------------------------------------
Set BaseFileName
@param input baseFileName
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int setBaseFileName( const std::string& baseFileName );
/**---------------------------------------------------------------------------------------
Get OutputFileFrequency
@return outputFileFrequency
--------------------------------------------------------------------------------------- */
int getOutputFileFrequency( void ) const;
/**---------------------------------------------------------------------------------------
Set OutputFileFrequency
@param input outputFileFrequency
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int setOutputFileFrequency( int outputFileFrequency );
/**---------------------------------------------------------------------------------------
Read info file
@param infoFileName file name to read
@return CpuImplicitSolventCommon::DefaultReturn if ok; else CpuImplicitSolventCommon::ErrorReturn; if major
problem, program will exit
--------------------------------------------------------------------------------------- */
int readInfoFile( const std::string infoFileName );
/**---------------------------------------------------------------------------------------
Get output file name (helper method) (Simbios)
fileName = (inputFileName || getBaseFileName()) . getForceCallIndex() . suffix
if inputFileName is NULL, then use getBaseFileName() as base file name
if getForceCallIndex() > 0, insert '.getForceCallIndex()'
append suffix, if not NULL
@param inputFileName inputFileName
@param suffix file suffix
@return file name
--------------------------------------------------------------------------------------- */
std::string getOutputFileName( const std::string* inputFileName, const std::string* suffix ) const;
/**---------------------------------------------------------------------------------------
Write Tinker xyz file (Simbios)
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomNames atom names
@param header header
@param xyzFileName output file name
@param bondsArray bond array -- used to print 1-2 bonds
@return 0 unless error detected
Currently no attempt is made to get the atom name/type to accurately
reflect the Tinker names/types. Rather method is used to output atoms
in Gromacs order and then reorder those in a corresponding xyz file
w/ the correct atom names/types so that they match the Gromacs order
This makes it easier to compare results between Gromacs and Tinker
--------------------------------------------------------------------------------------- */
/*
static int writeXyzFile( int numberOfAtoms, const std::vector<OpenMM::RealVec>& atomCoordinates,
const char** atomNames,
const std::string& header, const std::string& xyzFileName,
const implicitSolventBonds** bondsArray ); */
}; };
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/gbsa/SimTKOpenMMWindowLinux.h deleted 100755 → 0
View file @ 398f0609
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __SimTKOpenMMWindowLinux_H_
#define __SimTKOpenMMWindowLinux_H__
#ifdef WIN32
#define FOPEN fopen_s
#else
#define FOPEN fopen
#endif
#endif // __SimTKOpenMMWindowLinux_H__
platforms/reference/src/gbsa/cpuObcInterface.cpp
View file @ 51475608
...@@ -105,10 +105,6 @@ cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM* obc ...@@ -105,10 +105,6 @@ cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM* obc
CpuImplicitSolvent::setCpuImplicitSolvent( cpuObc ); CpuImplicitSolvent::setCpuImplicitSolvent( cpuObc );
// set base file name, ...
//cpuObc->readInfoFile( "CpuImplicitSolventInfo" );
// include/do not include ACE approximation (nonpolar solvation) // include/do not include ACE approximation (nonpolar solvation)
cpuObc->setIncludeAceApproximation( includeAceApproximation ); cpuObc->setIncludeAceApproximation( includeAceApproximation );
......
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