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mmeineke |
1052 |
#define _FILE_OFFSET_BITS 64 |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <sys/types.h> |
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#include <sys/stat.h> |
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#include <string.h> |
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#include "params.h" |
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#include "tcProps.h" |
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#include "readWrite.h" |
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mmeineke |
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#define BUFFER_SIZE 2000 |
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int isScanned; |
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mmeineke |
1056 |
int fileOpen; |
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int nFrames; |
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double *frameTimes; |
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mmeineke |
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FILE* inFile; |
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char* inName; |
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|
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struct linkedPos{ |
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fpos_t *myPos; |
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double timeStamp; |
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double Hmat[3][3]; |
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struct linkedPos* next; |
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}; |
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struct staticPos{ |
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fpos_t *myPos; |
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double Hmat[3][3]; |
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}; |
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struct staticPos* posArray; |
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void parseDumpLine( char readBuffer[BUFFER_SIZE], int index, |
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struct atomCoord* atoms ); |
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1058 |
void setU( double q[4], double u[3] ); |
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void normalizeQ( double q[4] ); |
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|
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mmeineke |
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void openFile( void ){ |
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mmeineke |
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|
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inFile = fopen(inName, "r"); |
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mmeineke |
1056 |
if(inFile ==NULL){ |
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fprintf(stderr, |
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"Error opening file \"%s\"\n", |
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inName); |
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exit(0); |
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} |
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fileOpen = 1; |
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} |
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mmeineke |
1052 |
void closeFile( void ){ |
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fclose( inFile ); |
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fileOpen = 0; |
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} |
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void setFrames( void ){ |
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|
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int i,j,k; |
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struct linkedPos* headPos; |
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struct linkedPos* currPos; |
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fpos_t *currPT; |
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mmeineke |
1053 |
char readBuffer[BUFFER_SIZE]; |
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mmeineke |
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char trash[BUFFER_SIZE]; |
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char* foo; |
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int lineNum = 0; |
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mmeineke |
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if( !fileOpen ){ |
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mmeineke |
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fprintf(stderr, |
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"Attempt to scan the file without first opening the file.\n" ); |
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exit(0); |
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} |
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|
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nFrames = 0; |
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headPos = (struct linkedPos*)malloc(sizeof(struct linkedPos)); |
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currPos = headPos; |
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|
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currPT = (fpos_t *)malloc(sizeof(fpos_t)); |
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fgetpos(inFile, currPT); |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
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if( feof( inFile ) ){ |
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fprintf( stderr, |
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"File \"%s\" ended unexpectedly at line %d\n", |
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inName, |
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lineNum ); |
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exit(0); |
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} |
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mmeineke |
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while( !feof( inFile ) ){ |
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currPos->next = (struct linkedPos*)malloc(sizeof(struct linkedPos)); |
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currPos = currPos->next; |
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currPos->myPos = currPT; |
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nFrames++; |
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i = atoi(readBuffer); |
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mmeineke |
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|
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
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if( feof( inFile ) ){ |
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fprintf( stderr, |
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"File \"%s\" ended unexpectedly at line %d\n", |
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inName, |
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lineNum ); |
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exit(0); |
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} |
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mmeineke |
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|
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// parse the comment line |
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foo = strtok(readBuffer, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading time from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->timeStamp = atof( foo ); |
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// get the Hx vector |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading Hx[0] from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->Hmat[0][0] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading Hx[1] from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->Hmat[1][0] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading Hx[2] from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->Hmat[2][0] = atof( foo ); |
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// get the Hy vector |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading Hy[0] from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->Hmat[0][1] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading Hy[1] from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->Hmat[1][1] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading Hy[2] from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->Hmat[2][1] = atof( foo ); |
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// get the Hz vector |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading Hz[0] from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->Hmat[0][2] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading Hz[1] from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->Hmat[1][2] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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fprintf(stderr, |
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"error in reading Hz[2] from %s at line %d\n", |
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inName, lineNum ); |
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exit(0); |
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} |
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currPos->Hmat[2][2] = atof( foo ); |
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// skip the atoms |
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for(j=0; j<i; j++){ |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
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if( feof( inFile ) ){ |
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fprintf( stderr, |
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"File \"%s\" ended unexpectedly at line %d," |
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" with atom %d\n", |
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inName, |
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lineNum, |
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j ); |
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exit(0); |
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} |
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} |
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mmeineke |
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currPT = (fpos_t *)malloc(sizeof(fpos_t)); |
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fgetpos(inFile, currPT); |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
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} |
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mmeineke |
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// allocate the static position array |
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mmeineke |
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|
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posArray = (struct staticPos*)calloc(nFrames, sizeof(struct staticPos)); |
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frameTimes = (double *)calloc(nFrames, sizeof(double) ); |
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i=0; |
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currPos = headPos->next; |
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while( currPos != NULL ){ |
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if(i>=nFrames){ |
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fprintf( stderr, |
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"The number of frame pointers exceeded the number of frames.\n" |
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" OOPS!\n" ); |
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exit(0); |
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} |
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frameTimes[i] = currPos->timeStamp; |
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posArray[i].myPos = currPos->myPos; |
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for(j=0;j<3;j++){ |
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for(k=0;k<3;k++){ |
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posArray[i].Hmat[j][k] = currPos->Hmat[j][k]; |
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} |
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} |
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i++; |
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currPos = currPos->next; |
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} |
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// clean up the linked list |
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currPos = headPos; |
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while( currPos != NULL ){ |
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headPos = currPos; |
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currPos = headPos->next; |
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free(headPos); |
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} |
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mmeineke |
1052 |
isScanned = 1; |
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} |
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mmeineke |
1056 |
|
283 |
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void readFrame(int theFrame, struct atomCoord* atoms, double Hmat[3][3] ){ |
285 |
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286 |
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// list of 'a priori' constants |
287 |
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288 |
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const int nLipAtoms = NL_ATOMS; |
289 |
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const int nBonds = NBONDS; |
290 |
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const int nLipids = NLIPIDS; |
291 |
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const int nSSD = NSSD; |
292 |
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const int nAtoms = nLipAtoms * nLipids + nSSD; |
293 |
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294 |
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fpos_t *framePos; |
295 |
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char readBuffer[BUFFER_SIZE]; |
296 |
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297 |
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int i, j, k; |
298 |
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299 |
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300 |
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// quick checks |
301 |
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302 |
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if (theFrame >= nFrames){ |
303 |
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304 |
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fprintf(stderr, |
305 |
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"frame %d, is out of range\n", |
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theFrame ); |
307 |
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exit(0); |
308 |
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} |
309 |
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310 |
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if( !fileOpen ){ |
311 |
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312 |
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fprintf( stderr, |
313 |
mmeineke |
1060 |
"File is closed, cannot read frame %d.\n", |
314 |
mmeineke |
1056 |
theFrame ); |
315 |
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exit(0); |
316 |
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} |
317 |
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318 |
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// access the frame |
319 |
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320 |
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framePos = posArray[theFrame].myPos; |
321 |
mmeineke |
1060 |
fsetpos( inFile, framePos ); |
322 |
mmeineke |
1056 |
|
323 |
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for(j=0;j<3;j++){ |
324 |
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for(k=0;k<3;k++){ |
325 |
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Hmat[j][k] = posArray[theFrame].Hmat[j][k]; |
326 |
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} |
327 |
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} |
328 |
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329 |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
330 |
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if( feof( inFile ) ){ |
331 |
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fprintf( stderr, |
332 |
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"File \"%s\" ended unexpectedly in Frame %d\n", |
333 |
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inName, |
334 |
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theFrame ); |
335 |
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exit(0); |
336 |
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} |
337 |
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338 |
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i = atoi( readBuffer ); |
339 |
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if( i != nAtoms ){ |
340 |
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fprintf( stderr, |
341 |
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"Error in frame %d: frame atoms, %d, does not params atoms, %d\n", |
342 |
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theFrame, |
343 |
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i, |
344 |
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nAtoms ); |
345 |
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exit(0); |
346 |
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} |
347 |
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348 |
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// read and toss the comment line |
349 |
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350 |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
351 |
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if( feof( inFile ) ){ |
352 |
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fprintf( stderr, |
353 |
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"File \"%s\" ended unexpectedly in Frame %d\n", |
354 |
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inName, |
355 |
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theFrame ); |
356 |
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exit(0); |
357 |
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} |
358 |
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359 |
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// read the atoms |
360 |
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361 |
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for( i=0; i < nAtoms; i++){ |
362 |
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363 |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
364 |
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if( feof( inFile ) ){ |
365 |
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fprintf( stderr, |
366 |
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"File \"%s\" ended unexpectedly in Frame %d at atom %d\n", |
367 |
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inName, |
368 |
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theFrame, |
369 |
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i ); |
370 |
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exit(0); |
371 |
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} |
372 |
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373 |
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374 |
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parseDumpLine( readBuffer, i, atoms ); |
375 |
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} |
376 |
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} |
377 |
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378 |
mmeineke |
1058 |
void parseDumpLine( char readLine[BUFFER_SIZE], int i, |
379 |
mmeineke |
1056 |
struct atomCoord* atoms ){ |
380 |
mmeineke |
1060 |
|
381 |
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const int nLipAtoms = NL_ATOMS; |
382 |
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const int nBonds = NBONDS; |
383 |
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const int nLipids = NLIPIDS; |
384 |
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const int nSSD = NSSD; |
385 |
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const int nAtoms = nLipAtoms * nLipids + nSSD; |
386 |
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|
387 |
mmeineke |
1056 |
char* foo; |
388 |
|
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double q[4]; |
389 |
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|
390 |
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// set the string tokenizer |
391 |
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392 |
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foo = strtok(readLine, " ,;\t"); |
393 |
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394 |
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// check the atom ID |
395 |
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|
396 |
mmeineke |
1058 |
switch( atoms[i].type ){ |
397 |
mmeineke |
1056 |
|
398 |
|
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case HEAD: |
399 |
|
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if( strcmp(foo, "HEAD") ){ |
400 |
|
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fprintf( stderr, |
401 |
mmeineke |
1060 |
"Atom %s does not match master array type \"HEAD\".\n", |
402 |
mmeineke |
1056 |
foo ); |
403 |
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exit(0); |
404 |
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} |
405 |
|
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break; |
406 |
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|
407 |
|
|
case CH: |
408 |
|
|
if( strcmp(foo, "CH") ){ |
409 |
|
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fprintf( stderr, |
410 |
mmeineke |
1060 |
"Atom %s does not match master array type \"CH\".\n", |
411 |
mmeineke |
1056 |
foo ); |
412 |
|
|
exit(0); |
413 |
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|
} |
414 |
|
|
break; |
415 |
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|
416 |
|
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case CH2: |
417 |
|
|
if( strcmp(foo, "CH2") ){ |
418 |
|
|
fprintf( stderr, |
419 |
mmeineke |
1060 |
"Atom %s does not match master array type \"CH2\".\n", |
420 |
mmeineke |
1056 |
foo ); |
421 |
|
|
exit(0); |
422 |
|
|
} |
423 |
|
|
break; |
424 |
|
|
|
425 |
|
|
case CH3: |
426 |
|
|
if( strcmp(foo, "CH3") ){ |
427 |
|
|
fprintf( stderr, |
428 |
mmeineke |
1060 |
"Atom %s does not match master array type \"CH3\".\n", |
429 |
mmeineke |
1056 |
foo ); |
430 |
|
|
exit(0); |
431 |
|
|
} |
432 |
|
|
break; |
433 |
|
|
|
434 |
|
|
case SSD: |
435 |
|
|
if( strcmp(foo, "SSD") ){ |
436 |
|
|
fprintf( stderr, |
437 |
mmeineke |
1060 |
"Atom %s does not match master array type \"SSD\".\n", |
438 |
mmeineke |
1056 |
foo ); |
439 |
|
|
exit(0); |
440 |
|
|
} |
441 |
|
|
break; |
442 |
|
|
|
443 |
|
|
default: |
444 |
|
|
fprintf(stderr, |
445 |
|
|
"Atom %d is an unrecognized enumeration\n", |
446 |
mmeineke |
1058 |
i ); |
447 |
mmeineke |
1056 |
exit(0); |
448 |
|
|
} |
449 |
|
|
|
450 |
|
|
// get the positions |
451 |
|
|
|
452 |
|
|
foo = strtok(NULL, " ,;\t"); |
453 |
|
|
if(foo == NULL){ |
454 |
|
|
fprintf( stderr, |
455 |
|
|
"error in reading postition x from %s\n" |
456 |
mmeineke |
1058 |
"natoms = %d, i = %d\n", |
457 |
|
|
inName, nAtoms, i ); |
458 |
mmeineke |
1056 |
exit(0); |
459 |
|
|
} |
460 |
|
|
atoms[i].pos[0] = atof( foo ); |
461 |
|
|
|
462 |
|
|
foo = strtok(NULL, " ,;\t"); |
463 |
|
|
if(foo == NULL){ |
464 |
|
|
fprintf( stderr, |
465 |
|
|
"error in reading postition y from %s\n" |
466 |
mmeineke |
1058 |
"natoms = %d, i = %d\n", |
467 |
|
|
inName, nAtoms, i ); |
468 |
mmeineke |
1056 |
exit(0); |
469 |
|
|
} |
470 |
|
|
atoms[i].pos[1] = atof( foo ); |
471 |
|
|
|
472 |
|
|
foo = strtok(NULL, " ,;\t"); |
473 |
|
|
if(foo == NULL){ |
474 |
|
|
fprintf( stderr, |
475 |
|
|
"error in reading postition z from %s\n" |
476 |
mmeineke |
1058 |
"natoms = %d, i = %d\n", |
477 |
|
|
inName, nAtoms, i ); |
478 |
mmeineke |
1056 |
exit(0); |
479 |
|
|
} |
480 |
|
|
atoms[i].pos[2] = atof( foo ); |
481 |
|
|
|
482 |
|
|
|
483 |
|
|
// get the velocities |
484 |
|
|
|
485 |
|
|
foo = strtok(NULL, " ,;\t"); |
486 |
|
|
if(foo == NULL){ |
487 |
|
|
fprintf( stderr, |
488 |
|
|
"error in reading velocity x from %s\n" |
489 |
mmeineke |
1058 |
"natoms = %d, i = %d\n", |
490 |
|
|
inName, nAtoms, i ); |
491 |
mmeineke |
1056 |
exit(0); |
492 |
|
|
} |
493 |
|
|
atoms[i].vel[0] = atof( foo ); |
494 |
|
|
|
495 |
|
|
foo = strtok(NULL, " ,;\t"); |
496 |
|
|
if(foo == NULL){ |
497 |
|
|
fprintf( stderr, |
498 |
|
|
"error in reading velocity y from %s\n" |
499 |
mmeineke |
1058 |
"natoms = %d, i = %d\n", |
500 |
|
|
inName, nAtoms, i ); |
501 |
mmeineke |
1056 |
exit(0); |
502 |
|
|
} |
503 |
|
|
atoms[i].vel[1] = atof( foo ); |
504 |
|
|
|
505 |
|
|
foo = strtok(NULL, " ,;\t"); |
506 |
|
|
if(foo == NULL){ |
507 |
|
|
fprintf( stderr, |
508 |
|
|
"error in reading velocity z from %s\n" |
509 |
mmeineke |
1058 |
"natoms = %d, i = %d\n", |
510 |
|
|
inName, nAtoms, i ); |
511 |
mmeineke |
1056 |
exit(0); |
512 |
|
|
} |
513 |
|
|
atoms[i].vel[2] = atof( foo ); |
514 |
|
|
|
515 |
|
|
|
516 |
|
|
// get the quaternions |
517 |
|
|
|
518 |
|
|
if( (atoms[i].type == HEAD) || (atoms[i].type == SSD) ){ |
519 |
|
|
|
520 |
|
|
foo = strtok(NULL, " ,;\t"); |
521 |
|
|
if(foo == NULL){ |
522 |
mmeineke |
1060 |
fprintf( stderr, |
523 |
|
|
"error in reading quaternion 0 from %s\n" |
524 |
|
|
"natoms = %d, i = %d\n", |
525 |
|
|
inName, nAtoms, i ); |
526 |
mmeineke |
1056 |
exit(0); |
527 |
|
|
} |
528 |
|
|
q[0] = atof( foo ); |
529 |
|
|
|
530 |
|
|
foo = strtok(NULL, " ,;\t"); |
531 |
|
|
if(foo == NULL){ |
532 |
|
|
fprintf( stderr, |
533 |
|
|
"error in reading quaternion 1 from %s\n" |
534 |
mmeineke |
1058 |
"natoms = %d, i = %d\n", |
535 |
|
|
inName, nAtoms, i ); |
536 |
mmeineke |
1056 |
exit(0); |
537 |
|
|
} |
538 |
|
|
q[1] = atof( foo ); |
539 |
|
|
|
540 |
|
|
foo = strtok(NULL, " ,;\t"); |
541 |
|
|
if(foo == NULL){ |
542 |
|
|
fprintf( stderr, |
543 |
|
|
"error in reading quaternion 2 from %s\n" |
544 |
mmeineke |
1058 |
"natoms = %d, i = %d\n", |
545 |
|
|
inName, nAtoms, i ); |
546 |
mmeineke |
1056 |
exit(0); |
547 |
|
|
} |
548 |
|
|
q[2] = atof( foo ); |
549 |
|
|
|
550 |
|
|
foo = strtok(NULL, " ,;\t"); |
551 |
|
|
if(foo == NULL){ |
552 |
|
|
fprintf( stderr, |
553 |
|
|
"error in reading quaternion 3 from %s\n" |
554 |
mmeineke |
1058 |
"natoms = %d, i = %d\n", |
555 |
|
|
inName, nAtoms, i ); |
556 |
mmeineke |
1056 |
exit(0); |
557 |
|
|
} |
558 |
|
|
q[3] = atof( foo ); |
559 |
mmeineke |
1058 |
|
560 |
|
|
normalizeQ( q ); |
561 |
|
|
|
562 |
|
|
setU( q, atoms[i].u ); |
563 |
mmeineke |
1056 |
} |
564 |
mmeineke |
1058 |
} |
565 |
mmeineke |
1056 |
|
566 |
|
|
|
567 |
mmeineke |
1058 |
void setU( double the_q[4], double u[3] ){ |
568 |
mmeineke |
1056 |
|
569 |
mmeineke |
1058 |
double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
570 |
|
|
double A[3][3]; |
571 |
|
|
double rb[3]; |
572 |
mmeineke |
1060 |
int i,j,k; |
573 |
mmeineke |
1056 |
|
574 |
mmeineke |
1058 |
// initialize the axis |
575 |
mmeineke |
1056 |
|
576 |
mmeineke |
1058 |
rb[0] = 0.0; |
577 |
|
|
rb[1] = 0.0; |
578 |
|
|
rb[2] = 1.0; |
579 |
|
|
|
580 |
|
|
// set the rotation matrix |
581 |
|
|
|
582 |
|
|
q0Sqr = the_q[0] * the_q[0]; |
583 |
|
|
q1Sqr = the_q[1] * the_q[1]; |
584 |
|
|
q2Sqr = the_q[2] * the_q[2]; |
585 |
|
|
q3Sqr = the_q[3] * the_q[3]; |
586 |
|
|
|
587 |
|
|
A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
588 |
|
|
A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
589 |
|
|
A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
590 |
|
|
|
591 |
|
|
A[1][0] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
592 |
|
|
A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
593 |
|
|
A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
594 |
|
|
|
595 |
|
|
A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
596 |
|
|
A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
597 |
|
|
A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
598 |
|
|
|
599 |
|
|
// perform the rotation |
600 |
|
|
|
601 |
|
|
for( i=0; i<3; i++ ){ |
602 |
|
|
u[i] = 0.0; |
603 |
|
|
|
604 |
|
|
for( j=0; j<3; j++ ){ |
605 |
|
|
u[i] += A[j][i] * rb[j]; |
606 |
|
|
} |
607 |
|
|
} |
608 |
mmeineke |
1056 |
} |
609 |
mmeineke |
1058 |
|
610 |
|
|
void normalizeQ( double q[4] ){ |
611 |
|
|
|
612 |
|
|
double qSqr, qL; |
613 |
|
|
int i; |
614 |
|
|
|
615 |
|
|
qSqr = 0.0; |
616 |
|
|
for(i=0;i<4;i++) |
617 |
|
|
qSqr += q[i] * q[i]; |
618 |
|
|
|
619 |
|
|
for(i=0;i<4;i++) |
620 |
|
|
q[i] /= qSqr; |
621 |
|
|
} |
622 |
mmeineke |
1080 |
|
623 |
|
|
double scanSmallestZ(int startFrame){ |
624 |
|
|
double smallest; |
625 |
|
|
int i; |
626 |
|
|
|
627 |
|
|
smallest = posArray[startFrame].Hmat[2][2]; |
628 |
|
|
for(i=startFrame;i<nFrames;i++) |
629 |
|
|
smallest = |
630 |
|
|
(smallest<posArray[i].Hmat[2][2])? smallest : posArray[i].Hmat[2][2]; |
631 |
|
|
|
632 |
|
|
return smallest; |
633 |
|
|
} |
634 |
|
|
|
635 |
mmeineke |
1058 |
|