| 5 |
|
#include <string> |
| 6 |
|
|
| 7 |
|
#include "SimSetup.hpp" |
| 8 |
+ |
#include "ReadWrite.hpp" |
| 9 |
|
#include "parse_me.h" |
| 10 |
|
#include "Integrator.hpp" |
| 11 |
|
#include "simError.h" |
| 97 |
|
int i, j, k, globalAtomIndex; |
| 98 |
|
|
| 99 |
|
// gather all of the information from the Bass file |
| 100 |
< |
|
| 100 |
> |
|
| 101 |
> |
std::cerr << "gathering info\n"; |
| 102 |
> |
|
| 103 |
|
gatherInfo(); |
| 104 |
|
|
| 105 |
|
// creation of complex system objects |
| 106 |
|
|
| 107 |
+ |
std::cerr << "creating system objects\n"; |
| 108 |
+ |
|
| 109 |
|
sysObjectsCreation(); |
| 110 |
|
|
| 111 |
|
// check on the post processing info |
| 112 |
|
|
| 113 |
+ |
std::cerr << "performing final info check.\n"; |
| 114 |
+ |
|
| 115 |
|
finalInfoCheck(); |
| 116 |
|
|
| 117 |
|
// initialize the system coordinates |
| 118 |
+ |
|
| 119 |
+ |
std::cerr << "about to init coords\n"; |
| 120 |
|
|
| 121 |
|
if( !isInfoArray ) initSystemCoords(); |
| 122 |
|
|
| 897 |
|
void SimSetup::initSystemCoords( void ){ |
| 898 |
|
int i; |
| 899 |
|
|
| 900 |
+ |
char* inName; |
| 901 |
+ |
|
| 902 |
|
std::cerr << "Setting atom Coords\n"; |
| 903 |
|
|
| 904 |
|
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
| 911 |
|
#ifdef IS_MPI // is_mpi |
| 912 |
|
if( worldRank == 0 ){ |
| 913 |
|
#endif //is_mpi |
| 914 |
< |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
| 914 |
> |
inName = globals->getInitialConfig(); |
| 915 |
> |
fileInit = new InitializeFromFile( inName ); |
| 916 |
|
#ifdef IS_MPI |
| 917 |
|
}else fileInit = new InitializeFromFile( NULL ); |
| 918 |
|
#endif |
| 1045 |
|
int i,k; |
| 1046 |
|
|
| 1047 |
|
// create the forceField |
| 1048 |
< |
|
| 1048 |
> |
|
| 1049 |
|
createFF(); |
| 1050 |
|
|
| 1051 |
|
// extract componentList |
| 1063 |
|
#endif //is_mpi |
| 1064 |
|
|
| 1065 |
|
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
| 1066 |
< |
|
| 1066 |
> |
|
| 1067 |
|
makeSysArrays(); |
| 1068 |
|
|
| 1069 |
|
// make and initialize the molecules (all but atomic coordinates) |
| 1070 |
< |
|
| 1070 |
> |
|
| 1071 |
|
makeMolecules(); |
| 1072 |
|
|
| 1073 |
|
for(k=0; k<nInfo; k++){ |
