| 1 |
mmeineke |
821 |
#include <iostream> |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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#include "simError.h" |
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#include "SimInfo.hpp" |
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#include "ReadWrite.hpp" |
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#include "MoLocator.hpp" |
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#include "latticeBuilder.hpp" |
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#include "QuickBass.hpp" |
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#define VERSION_MAJOR 0 |
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#define VERSION_MINOR 1 |
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char *programName; /*the name of the program */ |
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void usage(void); |
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int buildLatticeBilayer( double aLat, |
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double bLat, |
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double leafSpacing); |
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using namespace std; |
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int main(int argC,char* argV[]){ |
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int i,j; // loop counters |
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char* outPrefix; // the output prefix |
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char* conversionCheck; |
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bool conversionError; |
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bool optionError; |
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char currentFlag; // used in parsing the flags |
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bool done = false; // multipurpose boolean |
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bool havePrefix; // boolean for the output prefix |
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char* lipidName; |
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char* waterName; |
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bool haveWaterName, haveLipidName; |
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bool haveSpacing, haveAlat, haveBlat; |
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double aLat, bLat, leafSpacing; |
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char* inName; |
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// first things first, all of the initializations |
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fflush(stdout); |
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srand48( 1337 ); // the random number generator. |
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initSimError(); // the error handler |
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outPrefix = NULL; |
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inName = NULL; |
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conversionError = false; |
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optionError = false; |
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havePrefix = false; |
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haveAlat = false; |
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haveBlat = false; |
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haveSpacing = false; |
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programName = argV[0]; /*save the program name in case we need it*/ |
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for( i = 1; i < argC; i++){ |
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if(argV[i][0] =='-'){ |
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// parse the option |
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if(argV[i][1] == '-' ){ |
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// parse long word options |
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if( !strcmp( argV[i], "--version") ){ |
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printf("\n" |
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"staticProps version %d.%d\n" |
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"\n", |
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VERSION_MAJOR, VERSION_MINOR ); |
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exit(0); |
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} |
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else if( !strcmp( argV[i], "--help") ){ |
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usage(); |
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exit(0); |
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} |
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// anything else is an error |
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else{ |
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fprintf( stderr, |
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"Invalid option \"%s\"\n", argV[i] ); |
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usage(); |
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exit(0); |
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} |
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} |
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else{ |
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// parse single character options |
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done =0; |
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j = 1; |
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currentFlag = argV[i][j]; |
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while( (currentFlag != '\0') && (!done) ){ |
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switch(currentFlag){ |
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case 'o': |
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// -o <prefix> => the output prefix. |
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j++; |
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currentFlag = argV[i][j]; |
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if( currentFlag != '\0' ) optionError = true; |
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if( optionError ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"The -o flag should end an option sequence.\n" |
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" example: -r <outname> *NOT* -or <outname>\n" ); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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i++; |
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if( i>=argC ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"not enough arguments for -o\n"); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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outPrefix = argV[i]; |
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if( outPrefix[0] == '-' ) optionError = true; |
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if( optionError ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"\"%s\" is not a valid out prefix/name.\n" |
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"Out prefix/name should not begin with a dash.\n", |
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outPrefix ); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
| 155 |
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| 156 |
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havePrefix = true; |
| 157 |
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done = true; |
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break; |
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| 160 |
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case 'l': |
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// -l <lipidName> => the lipid name. |
| 162 |
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| 163 |
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j++; |
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currentFlag = argV[i][j]; |
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| 166 |
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if( currentFlag != '\0' ) optionError = true; |
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| 168 |
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if( optionError ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"The -l flag should end an option sequence.\n" |
| 172 |
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" example: -rl <lipidName> *NOT* -lr <lipidName>\n" ); |
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usage(); |
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painCave.isFatal = 1; |
| 175 |
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simError(); |
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} |
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| 178 |
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i++; |
| 179 |
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if( i>=argC ){ |
| 180 |
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sprintf( painCave.errMsg, |
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"\n" |
| 182 |
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"not enough arguments for -l\n"); |
| 183 |
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usage(); |
| 184 |
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painCave.isFatal = 1; |
| 185 |
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simError(); |
| 186 |
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} |
| 187 |
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| 188 |
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lipidName = argV[i]; |
| 189 |
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if( lipidName[0] == '-' ) optionError = true; |
| 190 |
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| 191 |
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if( optionError ){ |
| 192 |
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sprintf( painCave.errMsg, |
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"\n" |
| 194 |
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"\"%s\" is not a valid lipidName.\n" |
| 195 |
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"lipidName should not begin with a dash.\n", |
| 196 |
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lipidName ); |
| 197 |
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usage(); |
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painCave.isFatal = 1; |
| 199 |
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simError(); |
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} |
| 201 |
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haveLipidName = true; |
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done = true; |
| 204 |
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break; |
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| 206 |
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case 'w': |
| 207 |
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// -w <waterName> => the water name. |
| 208 |
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| 209 |
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j++; |
| 210 |
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currentFlag = argV[i][j]; |
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| 212 |
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if( currentFlag != '\0' ) optionError = true; |
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| 214 |
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if( optionError ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"The -w flag should end an option sequence.\n" |
| 218 |
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" example: -rw <waterName> *NOT* -lw <waterName>\n" ); |
| 219 |
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usage(); |
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painCave.isFatal = 1; |
| 221 |
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simError(); |
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} |
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| 224 |
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i++; |
| 225 |
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if( i>=argC ){ |
| 226 |
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sprintf( painCave.errMsg, |
| 227 |
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"\n" |
| 228 |
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"not enough arguments for -w\n"); |
| 229 |
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usage(); |
| 230 |
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painCave.isFatal = 1; |
| 231 |
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simError(); |
| 232 |
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} |
| 233 |
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| 234 |
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waterName = argV[i]; |
| 235 |
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if( waterName[0] == '-' ) optionError = true; |
| 236 |
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| 237 |
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if( optionError ){ |
| 238 |
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sprintf( painCave.errMsg, |
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"\n" |
| 240 |
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"\"%s\" is not a valid waterName.\n" |
| 241 |
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"waterName should not begin with a dash.\n", |
| 242 |
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waterName ); |
| 243 |
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usage(); |
| 244 |
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painCave.isFatal = 1; |
| 245 |
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simError(); |
| 246 |
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} |
| 247 |
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| 248 |
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haveWaterName = true; |
| 249 |
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done = true; |
| 250 |
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break; |
| 251 |
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| 252 |
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| 253 |
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case 'h': |
| 254 |
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// -h <double> set <double> to the hex lattice spacing |
| 255 |
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| 256 |
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haveAlat = true; |
| 257 |
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haveBlat = true; |
| 258 |
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j++; |
| 259 |
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currentFlag = argV[i][j]; |
| 260 |
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| 261 |
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if( currentFlag != '\0' ) optionError = true; |
| 262 |
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| 263 |
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if( optionError ){ |
| 264 |
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sprintf( painCave.errMsg, |
| 265 |
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"\n" |
| 266 |
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"The -h flag should end an option sequence.\n" |
| 267 |
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" example: -sh <double> *NOT* -hs <double>\n" ); |
| 268 |
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usage(); |
| 269 |
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painCave.isFatal = 1; |
| 270 |
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simError(); |
| 271 |
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} |
| 272 |
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| 273 |
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i++; |
| 274 |
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if( i>=argC ){ |
| 275 |
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sprintf( painCave.errMsg, |
| 276 |
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"\n" |
| 277 |
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"not enough arguments for -h\n"); |
| 278 |
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usage(); |
| 279 |
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painCave.isFatal = 1; |
| 280 |
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simError(); |
| 281 |
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} |
| 282 |
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| 283 |
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bLat = strtod( argV[i], &conversionCheck); |
| 284 |
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if( conversionCheck == argV[i] ) conversionError = true; |
| 285 |
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if( *conversionCheck != '\0' ) conversionError = true; |
| 286 |
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| 287 |
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if( conversionError ){ |
| 288 |
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sprintf( painCave.errMsg, |
| 289 |
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"Error converting \"%s\" to a double for \"h\".\n", |
| 290 |
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argV[i] ); |
| 291 |
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usage(); |
| 292 |
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painCave.isFatal = 1; |
| 293 |
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simError(); |
| 294 |
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} |
| 295 |
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| 296 |
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aLat = sqrt( 3.0 ) * bLat; |
| 297 |
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| 298 |
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done = true; |
| 299 |
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| 300 |
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break; |
| 301 |
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| 302 |
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case 'a': |
| 303 |
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// -a <double> set <double> to the aLat |
| 304 |
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| 305 |
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haveAlat = true; |
| 306 |
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j++; |
| 307 |
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currentFlag = argV[i][j]; |
| 308 |
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| 309 |
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if( currentFlag != '\0' ) optionError = true; |
| 310 |
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| 311 |
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if( optionError ){ |
| 312 |
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sprintf( painCave.errMsg, |
| 313 |
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"\n" |
| 314 |
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"The -a flag should end an option sequence.\n" |
| 315 |
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" example: -sa <double> *NOT* -as <double>\n" ); |
| 316 |
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usage(); |
| 317 |
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painCave.isFatal = 1; |
| 318 |
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simError(); |
| 319 |
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} |
| 320 |
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| 321 |
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i++; |
| 322 |
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if( i>=argC ){ |
| 323 |
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sprintf( painCave.errMsg, |
| 324 |
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"\n" |
| 325 |
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"not enough arguments for -a\n"); |
| 326 |
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usage(); |
| 327 |
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painCave.isFatal = 1; |
| 328 |
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simError(); |
| 329 |
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} |
| 330 |
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| 331 |
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aLat = strtod( argV[i], &conversionCheck); |
| 332 |
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if( conversionCheck == argV[i] ) conversionError = true; |
| 333 |
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if( *conversionCheck != '\0' ) conversionError = true; |
| 334 |
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| 335 |
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if( conversionError ){ |
| 336 |
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sprintf( painCave.errMsg, |
| 337 |
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"Error converting \"%s\" to a double for \"a\".\n", |
| 338 |
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argV[i] ); |
| 339 |
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usage(); |
| 340 |
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painCave.isFatal = 1; |
| 341 |
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simError(); |
| 342 |
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} |
| 343 |
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| 344 |
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done = true; |
| 345 |
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| 346 |
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break; |
| 347 |
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| 348 |
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case 'b': |
| 349 |
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// -b <double> set <double> to the bLat |
| 350 |
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| 351 |
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haveBlat = true; |
| 352 |
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j++; |
| 353 |
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currentFlag = argV[i][j]; |
| 354 |
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| 355 |
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if( currentFlag != '\0' ) optionError = true; |
| 356 |
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| 357 |
|
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if( optionError ){ |
| 358 |
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sprintf( painCave.errMsg, |
| 359 |
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"\n" |
| 360 |
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"The -b flag should end an option sequence.\n" |
| 361 |
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" example: -sb <double> *NOT* -bs <double>\n" ); |
| 362 |
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usage(); |
| 363 |
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painCave.isFatal = 1; |
| 364 |
|
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simError(); |
| 365 |
|
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} |
| 366 |
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| 367 |
|
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i++; |
| 368 |
|
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if( i>=argC ){ |
| 369 |
|
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sprintf( painCave.errMsg, |
| 370 |
|
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"\n" |
| 371 |
|
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"not enough arguments for -b\n"); |
| 372 |
|
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usage(); |
| 373 |
|
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painCave.isFatal = 1; |
| 374 |
|
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simError(); |
| 375 |
|
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} |
| 376 |
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| 377 |
|
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bLat = strtod( argV[i], &conversionCheck); |
| 378 |
|
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if( conversionCheck == argV[i] ) conversionError = true; |
| 379 |
|
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if( *conversionCheck != '\0' ) conversionError = true; |
| 380 |
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|
| 381 |
|
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if( conversionError ){ |
| 382 |
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sprintf( painCave.errMsg, |
| 383 |
|
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"Error converting \"%s\" to a double for \"a\".\n", |
| 384 |
|
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argV[i] ); |
| 385 |
|
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usage(); |
| 386 |
|
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painCave.isFatal = 1; |
| 387 |
|
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simError(); |
| 388 |
|
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} |
| 389 |
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| 390 |
|
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done = true; |
| 391 |
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|
| 392 |
|
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break; |
| 393 |
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|
| 394 |
|
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case 's': |
| 395 |
|
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// -s <double> set <double> to the leafSpacing |
| 396 |
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|
|
| 397 |
|
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haveSpacing = true; |
| 398 |
|
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j++; |
| 399 |
|
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currentFlag = argV[i][j]; |
| 400 |
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|
|
| 401 |
|
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if( currentFlag != '\0' ) optionError = true; |
| 402 |
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|
|
| 403 |
|
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if( optionError ){ |
| 404 |
|
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sprintf( painCave.errMsg, |
| 405 |
|
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"\n" |
| 406 |
|
|
"The -s flag should end an option sequence.\n" |
| 407 |
|
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" example: -rs <double> *NOT* -sr <double>\n" ); |
| 408 |
|
|
usage(); |
| 409 |
|
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painCave.isFatal = 1; |
| 410 |
|
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simError(); |
| 411 |
|
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} |
| 412 |
|
|
|
| 413 |
|
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i++; |
| 414 |
|
|
if( i>=argC ){ |
| 415 |
|
|
sprintf( painCave.errMsg, |
| 416 |
|
|
"\n" |
| 417 |
|
|
"not enough arguments for -s\n"); |
| 418 |
|
|
usage(); |
| 419 |
|
|
painCave.isFatal = 1; |
| 420 |
|
|
simError(); |
| 421 |
|
|
} |
| 422 |
|
|
|
| 423 |
|
|
leafSpacing = strtod( argV[i], &conversionCheck); |
| 424 |
|
|
if( conversionCheck == argV[i] ) conversionError = true; |
| 425 |
|
|
if( *conversionCheck != '\0' ) conversionError = true; |
| 426 |
|
|
|
| 427 |
|
|
if( conversionError ){ |
| 428 |
|
|
sprintf( painCave.errMsg, |
| 429 |
|
|
"Error converting \"%s\" to a double for \"s\".\n", |
| 430 |
|
|
argV[i] ); |
| 431 |
|
|
usage(); |
| 432 |
|
|
painCave.isFatal = 1; |
| 433 |
|
|
simError(); |
| 434 |
|
|
} |
| 435 |
|
|
|
| 436 |
|
|
done = true; |
| 437 |
|
|
|
| 438 |
|
|
break; |
| 439 |
|
|
|
| 440 |
|
|
default: |
| 441 |
|
|
|
| 442 |
|
|
sprintf(painCave.errMsg, |
| 443 |
|
|
"\n" |
| 444 |
|
|
"Bad option \"-%c\"\n", currentFlag); |
| 445 |
|
|
usage(); |
| 446 |
|
|
painCave.isFatal = 1; |
| 447 |
|
|
simError(); |
| 448 |
|
|
} |
| 449 |
|
|
j++; |
| 450 |
|
|
currentFlag = argV[i][j]; |
| 451 |
|
|
} |
| 452 |
|
|
} |
| 453 |
|
|
} |
| 454 |
|
|
|
| 455 |
|
|
else{ |
| 456 |
|
|
|
| 457 |
|
|
if( inName != NULL ){ |
| 458 |
|
|
sprintf( painCave.errMsg, |
| 459 |
|
|
"Error at \"%s\", program does not currently support\n" |
| 460 |
|
|
"more than one input bass file.\n" |
| 461 |
|
|
"\n", |
| 462 |
|
|
argV[i]); |
| 463 |
|
|
usage(); |
| 464 |
|
|
painCave.isFatal = 1; |
| 465 |
|
|
simError(); |
| 466 |
|
|
} |
| 467 |
|
|
|
| 468 |
|
|
inName = argV[i]; |
| 469 |
|
|
|
| 470 |
|
|
} |
| 471 |
|
|
} |
| 472 |
|
|
|
| 473 |
|
|
if( inName == NULL ){ |
| 474 |
|
|
sprintf( painCave.errMsg, |
| 475 |
|
|
"Error, bass file is needed to run.\n" ); |
| 476 |
|
|
usage(); |
| 477 |
|
|
painCave.isFatal = 1; |
| 478 |
|
|
simError(); |
| 479 |
|
|
} |
| 480 |
|
|
|
| 481 |
|
|
// if no output prefix is given default to "donkey". |
| 482 |
|
|
|
| 483 |
|
|
if( !havePrefix ){ |
| 484 |
|
|
outPrefix = strdup( "donkey" ); |
| 485 |
|
|
} |
| 486 |
|
|
|
| 487 |
|
|
|
| 488 |
|
|
if( !haveWaterName ){ |
| 489 |
|
|
sprintf( painCave.errMsg, |
| 490 |
|
|
"Error, the water name is needed to run.\n" |
| 491 |
|
|
); |
| 492 |
|
|
usage(); |
| 493 |
|
|
painCave.isFatal = 1; |
| 494 |
|
|
simError(); |
| 495 |
|
|
} |
| 496 |
|
|
|
| 497 |
|
|
if( !haveLipidName ){ |
| 498 |
|
|
sprintf( painCave.errMsg, |
| 499 |
|
|
"Error, the lipid name is needed to run.\n" |
| 500 |
|
|
); |
| 501 |
|
|
usage(); |
| 502 |
|
|
painCave.isFatal = 1; |
| 503 |
|
|
simError(); |
| 504 |
|
|
} |
| 505 |
|
|
|
| 506 |
|
|
if( !haveAlat ){ |
| 507 |
|
|
sprintf( painCave.errMsg, |
| 508 |
|
|
"Error, the hexagonal lattice parameter, a, is needed to run.\n" |
| 509 |
|
|
); |
| 510 |
|
|
usage(); |
| 511 |
|
|
painCave.isFatal = 1; |
| 512 |
|
|
simError(); |
| 513 |
|
|
} |
| 514 |
|
|
|
| 515 |
|
|
if( !haveBlat ){ |
| 516 |
|
|
sprintf( painCave.errMsg, |
| 517 |
|
|
"Error, the hexagonal lattice parameter, b, is needed to run.\n" |
| 518 |
|
|
); |
| 519 |
|
|
usage(); |
| 520 |
|
|
painCave.isFatal = 1; |
| 521 |
|
|
simError(); |
| 522 |
|
|
} |
| 523 |
|
|
|
| 524 |
|
|
|
| 525 |
|
|
if( !haveSpacing ){ |
| 526 |
|
|
sprintf( painCave.errMsg, |
| 527 |
|
|
"Error, the leaf spaceing is needed to run.\n" |
| 528 |
|
|
); |
| 529 |
|
|
usage(); |
| 530 |
|
|
painCave.isFatal = 1; |
| 531 |
|
|
simError(); |
| 532 |
|
|
} |
| 533 |
|
|
|
| 534 |
|
|
bsInfo.outPrefix = outPrefix; |
| 535 |
|
|
strcpy(bsInfo.waterName, waterName); |
| 536 |
|
|
strcpy(bsInfo.lipidName, lipidName); |
| 537 |
|
|
|
| 538 |
|
|
parseBuildBass( inName ); |
| 539 |
|
|
|
| 540 |
|
|
buildLatticeBilayer( aLat, bLat, leafSpacing ); |
| 541 |
|
|
|
| 542 |
|
|
return 0; |
| 543 |
|
|
} |
| 544 |
|
|
|
| 545 |
|
|
int buildLatticeBilayer(double aLat, |
| 546 |
|
|
double bLat, |
| 547 |
|
|
double leafSpacing){ |
| 548 |
|
|
|
| 549 |
|
|
typedef struct{ |
| 550 |
|
|
double rot[3][3]; |
| 551 |
|
|
double pos[3]; |
| 552 |
|
|
} coord; |
| 553 |
|
|
|
| 554 |
|
|
const double waterRho = 0.0334; // number density per cubic angstrom |
| 555 |
|
|
const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters |
| 556 |
|
|
|
| 557 |
|
|
double waterCell[3]; |
| 558 |
|
|
|
| 559 |
|
|
double *posX, *posY, *posZ; |
| 560 |
|
|
double pos[3], posA[3], posB[3]; |
| 561 |
|
|
|
| 562 |
|
|
const double waterFudge = 5.0; |
| 563 |
|
|
|
| 564 |
|
|
int i,j,k,l; |
| 565 |
|
|
int nAtoms, atomIndex, molIndex, molID; |
| 566 |
|
|
int* molSeq; |
| 567 |
|
|
int* molMap; |
| 568 |
|
|
int* molStart; |
| 569 |
|
|
int testTot, done; |
| 570 |
|
|
int nCells, nCellsX, nCellsY, nCellsZ; |
| 571 |
|
|
int nx, ny; |
| 572 |
|
|
double boxX, boxY, boxZ; |
| 573 |
|
|
double unitVector[3]; |
| 574 |
|
|
int which; |
| 575 |
|
|
int targetWaters; |
| 576 |
|
|
|
| 577 |
|
|
Atom** atoms; |
| 578 |
|
|
SimInfo* simnfo; |
| 579 |
|
|
SimInfo* testInfo; |
| 580 |
|
|
coord testSite; |
| 581 |
|
|
SimState* theConfig; |
| 582 |
|
|
DumpWriter* writer; |
| 583 |
|
|
|
| 584 |
|
|
MoleculeStamp* lipidStamp; |
| 585 |
|
|
MoleculeStamp* waterStamp; |
| 586 |
|
|
MoLocator *lipidLocate; |
| 587 |
|
|
MoLocator *waterLocate; |
| 588 |
|
|
int foundLipid, foundWater; |
| 589 |
|
|
int nLipids, lipidNatoms, nWaters, waterNatoms; |
| 590 |
|
|
int targetNlipids, targetNwaters; |
| 591 |
|
|
double targetWaterLipidRatio; |
| 592 |
|
|
double maxZ, minZ, zHeight; |
| 593 |
|
|
|
| 594 |
|
|
// create the simInfo objects |
| 595 |
|
|
|
| 596 |
|
|
simnfo = new SimInfo; |
| 597 |
|
|
|
| 598 |
|
|
// set the the lipidStamp |
| 599 |
|
|
|
| 600 |
|
|
foundLipid = 0; |
| 601 |
|
|
foundWater = 0; |
| 602 |
|
|
for(i=0; i<bsInfo.nComponents; i++){ |
| 603 |
|
|
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){ |
| 604 |
|
|
|
| 605 |
|
|
foundLipid = 1; |
| 606 |
|
|
lipidStamp = bsInfo.compStamps[i]; |
| 607 |
|
|
targetNlipids = bsInfo.componentsNmol[i]; |
| 608 |
|
|
lipidNatoms = lipidStamp->getNAtoms(); |
| 609 |
|
|
} |
| 610 |
|
|
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){ |
| 611 |
|
|
|
| 612 |
|
|
foundWater = 1; |
| 613 |
|
|
|
| 614 |
|
|
waterStamp = bsInfo.compStamps[i]; |
| 615 |
|
|
targetNwaters = bsInfo.componentsNmol[i]; |
| 616 |
|
|
waterNatoms = waterStamp->getNAtoms(); |
| 617 |
|
|
} |
| 618 |
|
|
} |
| 619 |
|
|
if( !foundLipid ){ |
| 620 |
|
|
sprintf(painCave.errMsg, |
| 621 |
|
|
"Could not find lipid \"%s\" in the bass file.\n", |
| 622 |
|
|
bsInfo.lipidName ); |
| 623 |
|
|
painCave.isFatal = 1; |
| 624 |
|
|
simError(); |
| 625 |
|
|
} |
| 626 |
|
|
if( !foundWater ){ |
| 627 |
|
|
sprintf(painCave.errMsg, |
| 628 |
|
|
"Could not find solvent \"%s\" in the bass file.\n", |
| 629 |
|
|
bsInfo.waterName ); |
| 630 |
|
|
painCave.isFatal = 1; |
| 631 |
|
|
simError(); |
| 632 |
|
|
} |
| 633 |
|
|
|
| 634 |
|
|
//create the Molocator arrays |
| 635 |
|
|
|
| 636 |
|
|
lipidLocate = new MoLocator( lipidStamp ); |
| 637 |
|
|
waterLocate = new MoLocator( waterStamp ); |
| 638 |
|
|
|
| 639 |
|
|
// gather info about the lipid |
| 640 |
|
|
|
| 641 |
|
|
testInfo = new SimInfo(); |
| 642 |
|
|
testInfo->n_atoms = lipidNatoms; |
| 643 |
|
|
theConfig = testInfo->getConfiguration(); |
| 644 |
|
|
theConfig->createArrays( lipidNatoms ); |
| 645 |
|
|
testInfo->atoms = new Atom*[lipidNatoms]; |
| 646 |
|
|
atoms = testInfo->atoms; |
| 647 |
|
|
|
| 648 |
|
|
testSite.pos[0] = 0.0; |
| 649 |
|
|
testSite.pos[1] = 0.0; |
| 650 |
|
|
testSite.pos[2] = 0.0; |
| 651 |
|
|
|
| 652 |
|
|
unitVector[0] = 0.0; |
| 653 |
|
|
unitVector[1] = 0.0; |
| 654 |
|
|
unitVector[2] = 1.0; |
| 655 |
|
|
|
| 656 |
|
|
getUnitRot(unitVector, testSite.rot ); |
| 657 |
|
|
lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig ); |
| 658 |
|
|
|
| 659 |
|
|
minZ = 0.0; |
| 660 |
|
|
maxZ = 0.0; |
| 661 |
|
|
double myPos[3]; |
| 662 |
|
|
for(i=0;i<lipidNatoms;i++){ |
| 663 |
|
|
atoms[i]->getPos( myPos ); |
| 664 |
|
|
minZ = (minZ > myPos[2]) ? myPos[2] : minZ; |
| 665 |
|
|
maxZ = (maxZ < myPos[2]) ? myPos[2] : maxZ; |
| 666 |
|
|
} |
| 667 |
|
|
zHeight = maxZ - minZ; |
| 668 |
|
|
|
| 669 |
|
|
nCells = (int) sqrt( (double)targetNlipids * bLat / (4.0 * aLat) ); |
| 670 |
|
|
|
| 671 |
|
|
nx = nCells; |
| 672 |
|
|
ny = (int) ((double)nCells * aLat / bLat); |
| 673 |
|
|
|
| 674 |
|
|
boxX = nx * aLat; |
| 675 |
|
|
boxY = ny * bLat; |
| 676 |
|
|
|
| 677 |
|
|
nLipids = 4 * nx * ny; |
| 678 |
|
|
coord* lipidSites = new coord[nLipids]; |
| 679 |
|
|
|
| 680 |
|
|
unitVector[0] = 0.0; |
| 681 |
|
|
unitVector[1] = 0.0; |
| 682 |
|
|
|
| 683 |
|
|
which = 0; |
| 684 |
|
|
|
| 685 |
|
|
for (i = 0; i < nx; i++) { |
| 686 |
|
|
for (j = 0; j < ny; j++ ) { |
| 687 |
|
|
for (k = 0; k < 2; k++) { |
| 688 |
|
|
|
| 689 |
|
|
lipidSites[which].pos[0] = (double)i * aLat; |
| 690 |
|
|
lipidSites[which].pos[1] = (double)j * bLat; |
| 691 |
|
|
lipidSites[which].pos[2] = ((double)k - 0.5) * (leafSpacing - maxZ); |
| 692 |
|
|
|
| 693 |
|
|
unitVector[2] = 2.0 * (double)k - 1.0; |
| 694 |
|
|
|
| 695 |
|
|
getUnitRot( unitVector, lipidSites[which].rot ); |
| 696 |
|
|
|
| 697 |
|
|
which++; |
| 698 |
|
|
|
| 699 |
|
|
lipidSites[which].pos[0] = aLat * ((double)i + 0.5); |
| 700 |
|
|
lipidSites[which].pos[1] = bLat * ((double)j + 0.5); |
| 701 |
|
|
lipidSites[which].pos[2] = ((double)k - 0.5) * (leafSpacing - maxZ); |
| 702 |
|
|
|
| 703 |
|
|
unitVector[2] = 2.0 * (double)k - 1.0; |
| 704 |
|
|
|
| 705 |
|
|
getUnitRot( unitVector, lipidSites[which].rot ); |
| 706 |
|
|
|
| 707 |
|
|
which++; |
| 708 |
|
|
} |
| 709 |
|
|
} |
| 710 |
|
|
} |
| 711 |
|
|
|
| 712 |
|
|
targetWaterLipidRatio = (double)targetNwaters / (double)targetNlipids; |
| 713 |
|
|
|
| 714 |
|
|
targetWaters = targetWaterLipidRatio * nLipids; |
| 715 |
|
|
|
| 716 |
|
|
// guess the size of the water box |
| 717 |
|
|
|
| 718 |
|
|
nCellsX = (int)ceil(boxX / pow(waterVol, ( 1.0 / 3.0 )) ); |
| 719 |
|
|
nCellsY = (int)ceil(boxY / pow(waterVol, ( 1.0 / 3.0 )) ); |
| 720 |
|
|
|
| 721 |
|
|
done = 0; |
| 722 |
|
|
nCellsZ = 0; |
| 723 |
|
|
while( !done ){ |
| 724 |
|
|
|
| 725 |
|
|
nCellsZ++; |
| 726 |
|
|
testTot = 4 * nCellsX * nCellsY * nCellsZ; |
| 727 |
|
|
|
| 728 |
|
|
if( testTot >= targetWaters ) done = 1; |
| 729 |
|
|
} |
| 730 |
|
|
|
| 731 |
|
|
nWaters = nCellsX * nCellsY * nCellsZ * 4; |
| 732 |
|
|
|
| 733 |
|
|
coord* waterSites = new coord[nWaters]; |
| 734 |
|
|
|
| 735 |
|
|
waterCell[0] = boxX / nCellsX; |
| 736 |
|
|
waterCell[1] = boxY / nCellsY; |
| 737 |
|
|
waterCell[2] = 4.0 / (waterRho * waterCell[0] * waterCell[1]); |
| 738 |
|
|
|
| 739 |
|
|
Lattice *myORTHO; |
| 740 |
|
|
myORTHO = new Lattice( ORTHORHOMBIC_LATTICE_TYPE, waterCell); |
| 741 |
|
|
myORTHO->setStartZ( leafSpacing / 2.0 + waterFudge); |
| 742 |
|
|
|
| 743 |
|
|
boxZ = waterCell[2] * nCellsZ + leafSpacing; |
| 744 |
|
|
|
| 745 |
|
|
// create an fcc lattice in the water box. |
| 746 |
|
|
|
| 747 |
|
|
which = 0; |
| 748 |
|
|
for( i=0; i < nCellsX; i++ ){ |
| 749 |
|
|
for( j=0; j < nCellsY; j++ ){ |
| 750 |
|
|
for( k=0; k < nCellsZ; k++ ){ |
| 751 |
|
|
|
| 752 |
|
|
myORTHO->getLatticePoints(&posX, &posY, &posZ, i, j, k); |
| 753 |
|
|
for(l=0; l<4; l++){ |
| 754 |
|
|
waterSites[which].pos[0] = posX[l]; |
| 755 |
|
|
waterSites[which].pos[1] = posY[l]; |
| 756 |
|
|
waterSites[which].pos[2] = posZ[l]; |
| 757 |
|
|
which++; |
| 758 |
|
|
} |
| 759 |
|
|
} |
| 760 |
|
|
} |
| 761 |
|
|
} |
| 762 |
|
|
|
| 763 |
|
|
// create the real Atom arrays |
| 764 |
|
|
|
| 765 |
|
|
nAtoms = 0; |
| 766 |
|
|
molIndex = 0; |
| 767 |
|
|
molStart = new int[nLipids + nWaters]; |
| 768 |
|
|
|
| 769 |
|
|
for(j=0; j<nLipids; j++){ |
| 770 |
|
|
molStart[molIndex] = nAtoms; |
| 771 |
|
|
molIndex++; |
| 772 |
|
|
nAtoms += lipidNatoms; |
| 773 |
|
|
} |
| 774 |
|
|
|
| 775 |
|
|
for(j=0; j<nWaters; j++){ |
| 776 |
|
|
molStart[molIndex] = nAtoms; |
| 777 |
|
|
molIndex++; |
| 778 |
|
|
nAtoms += waterNatoms; |
| 779 |
|
|
} |
| 780 |
|
|
|
| 781 |
|
|
theConfig = simnfo->getConfiguration(); |
| 782 |
|
|
theConfig->createArrays( nAtoms ); |
| 783 |
|
|
simnfo->atoms = new Atom*[nAtoms]; |
| 784 |
|
|
atoms = simnfo->atoms; |
| 785 |
|
|
|
| 786 |
|
|
|
| 787 |
|
|
// wrap back to <0,0,0> as center |
| 788 |
|
|
|
| 789 |
|
|
double Hmat[3][3]; |
| 790 |
|
|
|
| 791 |
|
|
Hmat[0][0] = boxX; |
| 792 |
|
|
Hmat[0][1] = 0.0; |
| 793 |
|
|
Hmat[0][2] = 0.0; |
| 794 |
|
|
|
| 795 |
|
|
Hmat[1][0] = 0.0; |
| 796 |
|
|
Hmat[1][1] = boxY; |
| 797 |
|
|
Hmat[1][2] = 0.0; |
| 798 |
|
|
|
| 799 |
|
|
Hmat[2][0] = 0.0; |
| 800 |
|
|
Hmat[2][1] = 0.0; |
| 801 |
|
|
Hmat[2][2] = boxZ; |
| 802 |
|
|
|
| 803 |
|
|
bsInfo.boxX = boxX; |
| 804 |
|
|
bsInfo.boxY = boxY; |
| 805 |
|
|
bsInfo.boxZ = boxZ; |
| 806 |
|
|
|
| 807 |
|
|
simnfo->setBoxM( Hmat ); |
| 808 |
|
|
|
| 809 |
|
|
for(j=0;j<nLipids;j++) |
| 810 |
|
|
simnfo->wrapVector( lipidSites[j].pos ); |
| 811 |
|
|
|
| 812 |
|
|
for(j=0;j<nWaters;j++) |
| 813 |
|
|
simnfo->wrapVector( waterSites[j].pos ); |
| 814 |
|
|
|
| 815 |
|
|
// initialize lipid positions |
| 816 |
|
|
|
| 817 |
|
|
molIndex = 0; |
| 818 |
|
|
for(i=0; i<nLipids; i++ ){ |
| 819 |
|
|
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 820 |
|
|
molStart[molIndex], theConfig ); |
| 821 |
|
|
molIndex++; |
| 822 |
|
|
} |
| 823 |
|
|
|
| 824 |
|
|
// initialize the water positions |
| 825 |
|
|
|
| 826 |
|
|
for(i=0; i<nWaters; i++){ |
| 827 |
|
|
|
| 828 |
|
|
getRandomRot( waterSites[i].rot ); |
| 829 |
|
|
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
| 830 |
|
|
molStart[molIndex], theConfig ); |
| 831 |
|
|
molIndex++; |
| 832 |
|
|
} |
| 833 |
|
|
|
| 834 |
|
|
// set up the SimInfo object |
| 835 |
|
|
|
| 836 |
|
|
Hmat[0][0] = boxX; |
| 837 |
|
|
Hmat[0][1] = 0.0; |
| 838 |
|
|
Hmat[0][2] = 0.0; |
| 839 |
|
|
|
| 840 |
|
|
Hmat[1][0] = 0.0; |
| 841 |
|
|
Hmat[1][1] = boxY; |
| 842 |
|
|
Hmat[1][2] = 0.0; |
| 843 |
|
|
|
| 844 |
|
|
Hmat[2][0] = 0.0; |
| 845 |
|
|
Hmat[2][1] = 0.0; |
| 846 |
|
|
Hmat[2][2] = boxZ; |
| 847 |
|
|
|
| 848 |
|
|
|
| 849 |
|
|
bsInfo.boxX = boxX; |
| 850 |
|
|
bsInfo.boxY = boxY; |
| 851 |
|
|
bsInfo.boxZ = boxZ; |
| 852 |
|
|
|
| 853 |
|
|
simnfo->setBoxM( Hmat ); |
| 854 |
|
|
|
| 855 |
|
|
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 856 |
|
|
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 857 |
|
|
|
| 858 |
|
|
// set up the writer and write out |
| 859 |
|
|
|
| 860 |
|
|
writer = new DumpWriter( simnfo ); |
| 861 |
|
|
writer->writeFinal( 0.0 ); |
| 862 |
|
|
|
| 863 |
|
|
return 1; |
| 864 |
|
|
} |
| 865 |
|
|
|
| 866 |
|
|
|
| 867 |
|
|
/*************************************************************************** |
| 868 |
|
|
* prints out the usage for the command line arguments, then exits. |
| 869 |
|
|
***************************************************************************/ |
| 870 |
|
|
|
| 871 |
|
|
void usage(){ |
| 872 |
|
|
(void)fprintf(stdout, |
| 873 |
|
|
"\n" |
| 874 |
|
|
"The proper usage is: %s [options] <input_file>\n" |
| 875 |
|
|
"\n" |
| 876 |
|
|
"Options:\n" |
| 877 |
|
|
"\n" |
| 878 |
|
|
" short:\n" |
| 879 |
|
|
" ------\n" |
| 880 |
|
|
" -o <name> The output prefix\n" |
| 881 |
|
|
" -l <lipidName> The name of the lipid molecule specified in the BASS file.\n" |
| 882 |
|
|
" -w <waterName> The name of the water molecule specified in the BASS file.\n" |
| 883 |
|
|
" -s <double> The leaf spaceing of the bilayer.\n" |
| 884 |
|
|
" -a <double> The hexagonal lattice constant, a, for the bilayer leaf.\n" |
| 885 |
|
|
" -b <double> The hexagonal lattice constant, b, for the bilayer leaf.\n" |
| 886 |
|
|
" -h <double> Use to set a and b for a normal hex lattice with spacing <double>\n" |
| 887 |
|
|
|
| 888 |
|
|
"\n" |
| 889 |
|
|
" long:\n" |
| 890 |
|
|
" -----\n" |
| 891 |
|
|
|
| 892 |
|
|
" --version displays the version number\n" |
| 893 |
|
|
" --help displays this help message.\n" |
| 894 |
|
|
"\n" |
| 895 |
|
|
"\n", |
| 896 |
|
|
programName); |
| 897 |
|
|
} |
