122 |
|
|
123 |
|
void SimSetup::createSim(void){ |
124 |
|
|
125 |
< |
// gather all of the information from the Bass file |
125 |
> |
// gather all of the information from the meta-data file |
126 |
|
|
127 |
|
gatherInfo(); |
128 |
|
|
646 |
|
|
647 |
|
} |
648 |
|
|
649 |
< |
void SimSetup::initFromBass(void){ |
649 |
> |
void SimSetup::initFromMetaDataFile(void){ |
650 |
|
int i, j, k; |
651 |
|
int n_cells; |
652 |
|
double cellx, celly, cellz; |
769 |
|
current_atom = comp_stamps[current_comp]->getAtom(k); |
770 |
|
if (!current_atom->havePosition()){ |
771 |
|
sprintf(painCave.errMsg, |
772 |
< |
"SimSetup:initFromBass error.\n" |
772 |
> |
"SimSetup:initFromMetaData error.\n" |
773 |
|
"\tComponent %s, atom %s does not have a position specified.\n" |
774 |
|
"\tThe initialization routine is unable to give a start" |
775 |
|
" position.\n", |
1003 |
|
"\tKeyword useSolidThermInt was set to 'true' but\n" |
1004 |
|
"\tthermodynamicIntegrationLambda (and/or\n" |
1005 |
|
"\tthermodynamicIntegrationK) was not specified.\n" |
1006 |
< |
"\tPlease provide a lambda value and k value in your .md file.\n"); |
1006 |
> |
"\tPlease provide a lambda value and k value in your meta-data file.\n"); |
1007 |
|
painCave.isFatal = 1; |
1008 |
|
simError(); |
1009 |
|
} |
1012 |
|
if (globals->getUseSolidThermInt()) { |
1013 |
|
sprintf( painCave.errMsg, |
1014 |
|
"SimSetup Warning: It appears that you have both solid and\n" |
1015 |
< |
"\tliquid thermodynamic integration activated in your .md\n" |
1015 |
> |
"\tliquid thermodynamic integration activated in your meta-data\n" |
1016 |
|
"\tfile. To avoid confusion, specify only one technique in\n" |
1017 |
< |
"\tyour .md file. Liquid-state thermodynamic integration\n" |
1017 |
> |
"\tyour meta-data file. Liquid-state thermodynamic integration\n" |
1018 |
|
"\twill be assumed for the current simulation. If this is not\n" |
1019 |
|
"\twhat you desire, set useSolidThermInt to 'true' and\n" |
1020 |
< |
"\tuseLiquidThermInt to 'false' in your .md file.\n"); |
1020 |
> |
"\tuseLiquidThermInt to 'false' in your meta-data file.\n"); |
1021 |
|
painCave.isFatal = 0; |
1022 |
|
simError(); |
1023 |
|
} |
1032 |
|
"\tKeyword useLiquidThermInt was set to 'true' but\n" |
1033 |
|
"\tthermodynamicIntegrationLambda (and/or\n" |
1034 |
|
"\tthermodynamicIntegrationK) was not specified.\n" |
1035 |
< |
"\tPlease provide a lambda value and k value in your .md file.\n"); |
1035 |
> |
"\tPlease provide a lambda value and k value in your meta-data file.\n"); |
1036 |
|
painCave.isFatal = 1; |
1037 |
|
simError(); |
1038 |
|
} |
1041 |
|
sprintf(painCave.errMsg, |
1042 |
|
"SimSetup Warning: If you want to use Thermodynamic\n" |
1043 |
|
"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n" |
1044 |
< |
"\t'true' in your .md file. These keywords are set to\n" |
1044 |
> |
"\t'true' in your meta-data file. These keywords are set to\n" |
1045 |
|
"\t'false' by default, so your lambda and/or k values are\n" |
1046 |
|
"\tbeing ignored.\n"); |
1047 |
|
painCave.isFatal = 0; |
1136 |
|
} |
1137 |
|
|
1138 |
|
#ifdef IS_MPI |
1139 |
< |
strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
1139 |
> |
strcpy(checkPointMsg, "Successfully gathered all information from meta-data file\n"); |
1140 |
|
MPIcheckPoint(); |
1141 |
|
#endif // is_mpi |
1142 |
|
} |
1765 |
|
else{ |
1766 |
|
sprintf(painCave.errMsg, |
1767 |
|
"SimSetup error: If you use a constant pressure\n" |
1768 |
< |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1768 |
> |
"\tensemble, you must set targetPressure in the meta-data file.\n"); |
1769 |
|
painCave.isFatal = 1; |
1770 |
|
simError(); |
1771 |
|
} |
1816 |
|
else{ |
1817 |
|
sprintf(painCave.errMsg, |
1818 |
|
"SimSetup error: If you use a constant pressure\n" |
1819 |
< |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1819 |
> |
"\tensemble, you must set targetPressure in the meta-data file.\n"); |
1820 |
|
painCave.isFatal = 1; |
1821 |
|
simError(); |
1822 |
|
} |
1869 |
|
else{ |
1870 |
|
sprintf(painCave.errMsg, |
1871 |
|
"SimSetup error: If you use a constant pressure\n" |
1872 |
< |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1872 |
> |
"\tensemble, you must set targetPressure in the meta-data file.\n"); |
1873 |
|
painCave.isFatal = 1; |
1874 |
|
simError(); |
1875 |
|
} |