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Commit c150c4df authored by Peter Eastman's avatar Peter Eastman
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Attempting to fix incorrect file capitalization introduced by Windows

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platforms/reference/src/SimTKUtilities/SimTKOpenMMUtilities.h deleted 100755 → 0
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/* 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 __SimTKOpenMMUtilities_H_
#define __SimTKOpenMMUtilities_H_
// class of shared, static utility methods
#include "SimTKOpenMMCommon.h"
#include "../sfmt/SFMT.h"
#include <stdio.h>
#include <string.h>
#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();
}
/**---------------------------------------------------------------------------------------
Class of static methods to be shared
Most methods are standalone 'utility' methods
--------------------------------------------------------------------------------------- */
class SimTKOpenMMUtilities {
private:
static uint32_t _randomNumberSeed;
static bool _randomInitialized;
public:
// file flag enums
enum FileFlags { OpenDebugFile, WriteDebugFile, CloseDebugFile };
// dummy constructor/destructor
SimTKOpenMMUtilities(){};
~SimTKOpenMMUtilities(){};
/**---------------------------------------------------------------------------------------
Find distances**2 from a given atom (Simbios)
@param atomCoordinates atom coordinates
@param atomIndex atom index to find distances from
@param numberOfAtoms number of atoms
@param distances array of distances squared on @return; array size must be at least
numberOfAtoms
@param log if set, then print error messages to log file
@return distances
--------------------------------------------------------------------------------------- */
static int getDistanceSquaredFromSpecifiedAtom( RealOpenMM** atomCoordinates, int atomIndex,
int numberOfAtoms, RealOpenMM* distances,
FILE* log );
/**---------------------------------------------------------------------------------------
Find distances**2 from a given point (Simbios)
@param atomCoordinates atom coordinates
@param point point to find distances from
@param numberOfAtoms number of atoms
@param distances array of distances squared on @return; array size must be at least
numberOfAtoms
@param log if set, then print error messages to log file
@return distances
--------------------------------------------------------------------------------------- */
static int getDistanceSquaredFromSpecifiedPoint( RealOpenMM** atomCoordinates, RealOpenMM* point,
int numberOfAtoms, RealOpenMM* distances,
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 );
/**---------------------------------------------------------------------------------------
Allocate 1D RealOpenMM array (Simbios)
array[i]
@param iSize i-dimension
@param array1D array (if null on entry allocated)
@param initialize if true, then initialize array
@param initialValue intitial value
@param idString id string
@return array
--------------------------------------------------------------------------------------- */
static RealOpenMM* allocateOneDRealOpenMMArray( int iSize, RealOpenMM* array1D, int initialize,
RealOpenMM initialValue,
const std::string& idString = std::string( "1DArray" ) );
/**---------------------------------------------------------------------------------------
Allocate 2D RealOpenMM array (Simbios)
array[i][j]
@param iSize i-dimension
@param jSize j-dimension
@param array2D array (if null on entry allocated)
@param initialize if true, then initialize array
@param initialValue intitial value
@param idString id string
@return array
--------------------------------------------------------------------------------------- */
static RealOpenMM** allocateTwoDRealOpenMMArray( int iSize, int jSize,
RealOpenMM** array2D, int initialize,
RealOpenMM initialValue,
const std::string& idString = std::string( "2DArray" ) );
/* ---------------------------------------------------------------------------------------
Free 2D RealOpenMM array (Simbios)
array[i][j]
@param array2D array (if null on entry allocated)
@param idString id string
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int freeOneDRealOpenMMArray( RealOpenMM* array1D,
const std::string& idString = std::string( "1DArray" ) );
/* ---------------------------------------------------------------------------------------
Free 2D RealOpenMM array (Simbios)
array[i][j]
@param array2D array (if null on entry allocated)
@param idString id string
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
static int freeTwoDRealOpenMMArray( RealOpenMM** array2D,
const std::string& idString = std::string( "2DArray" ) );
/**---------------------------------------------------------------------------------------
Initialize 2D RealOpenMM array (Simbios)
array[i][j]
@param iSize i-dimension
@param jSize j-dimension
@param array2D array (if null on entry allocated)
@param initialValue intitial value
@return array
--------------------------------------------------------------------------------------- */
static int initialize2DRealOpenMMArray( int iSize, int jSize,
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
@param vectorZ = vectorX x vectorY
@param vectorX x-vector
@param vectorY y-vector
@param vectorZ z-vector
@return vector is 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, 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, 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 );
/**---------------------------------------------------------------------------------------
Get normally distributed random number
@return random value
--------------------------------------------------------------------------------------- */
static RealOpenMM getNormallyDistributedRandomNumber( void );
/**---------------------------------------------------------------------------------------
Get uniformly distributed random number in the range [0, 1)
@return random value
--------------------------------------------------------------------------------------- */
static RealOpenMM getUniformlyDistributedRandomNumber( void );
/**---------------------------------------------------------------------------------------
Get random number seed
@return random number seed
--------------------------------------------------------------------------------------- */
static uint32_t getRandomNumberSeed( void );
/**---------------------------------------------------------------------------------------
Set random number seed
@param seed new seed value
@return DefaultReturn
--------------------------------------------------------------------------------------- */
static void setRandomNumberSeed( uint32_t seed );
};
// ---------------------------------------------------------------------------------------
#endif // __SimTKOpenMMUtilities_H__
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