| version 1.1261 | version 1.1262 |
|---|
| |
| BigReal sumOfAs = 0; | BigReal sumOfAs = 0; |
| BigReal sumOfBs = 0; | BigReal sumOfBs = 0; |
| BigReal count = 0; // needed to avoid overflow | BigReal count = 0; // needed to avoid overflow |
| BigReal npairs = 0; | BigReal npairs; |
| for (int i=0; i < LJtypecount; i++) { | for (int i=0; i < LJtypecount; i++) { |
| if (numAtomsByLjType[i] > 1) { | |
| for (int j=0; j < LJtypecount; j++) { | for (int j=0; j < LJtypecount; j++) { |
| A = ATable[i*LJtypecount + j]; | A = ATable[i*LJtypecount + j]; |
| B = BTable[i*LJtypecount + j]; | B = BTable[i*LJtypecount + j]; |
| | if (!A && !B) continue; // don't count zeroed interactions |
| npairs = (numAtomsByLjType[i] - int(i==j))*BigReal(numAtomsByLjType[j]); | npairs = (numAtomsByLjType[i] - int(i==j))*BigReal(numAtomsByLjType[j]); |
| sumOfAs += npairs*A; | sumOfAs += npairs*A; |
| sumOfBs += npairs*B; | sumOfBs += npairs*B; |
| count += npairs; | count += npairs; |
| } | } |
| } | } |
| } | |
| delete [] numAtomsByLjType; | delete [] numAtomsByLjType; |
| delete [] ATable; | delete [] ATable; |
| delete [] BTable; | delete [] BTable; |
| |
| int alchFlagi = (get_fep_type(i) == 2 ? -1 : get_fep_type(i)); | int alchFlagi = (get_fep_type(i) == 2 ? -1 : get_fep_type(i)); |
| for (int j=i+1; j < numAtoms; ++j) { | for (int j=i+1; j < numAtoms; ++j) { |
| int alchFlagj = (get_fep_type(j) == 2 ? -1 : get_fep_type(j)); | int alchFlagj = (get_fep_type(j) == 2 ? -1 : get_fep_type(j)); |
| | int alchFlagSum = alchFlagi + alchFlagj; |
| | |
| // Ignore completely non-alchemical pairs. | // Ignore completely non-alchemical pairs. |
| if (alchFlagi == 0 && alchFlagj == 0) continue; | if (alchFlagi == 0 && alchFlagj == 0) continue; |
| | |
| |
| A = 4.0*sigma_ij*epsilon_ij*sigma_ij; | A = 4.0*sigma_ij*epsilon_ij*sigma_ij; |
| B = 4.0*sigma_ij*epsilon_ij; | B = 4.0*sigma_ij*epsilon_ij; |
| } | } |
| int alchFlagSum = alchFlagi + alchFlagj; | if (!A && !B) continue; // don't count zeroed interactions |
| | |
| if ( alchFlagSum > 0 ){ // in group 1, remove from group 2 | if ( alchFlagSum > 0 ){ // in group 1, remove from group 2 |
| sumOfAs2 -= 2*A; | sumOfAs2 -= 2*A; |
| sumOfBs2 -= 2*B; | sumOfBs2 -= 2*B; |
| |
| } | } |
| // This should save _tons_ of time, since the alchemical atoms are almost | // This should save _tons_ of time, since the alchemical atoms are almost |
| // always at the top of the pdb file. | // always at the top of the pdb file. |
| switch ( alchFlagi ){ | if ( alchFlagi == 1 || alchFlagi == -1 ) alch_counter++; |
| case -1: | |
| case 1: | |
| alch_counter++; | |
| break; | |
| } | |
| if ( alch_counter == (numFepInitial + numFepFinal) ) break; | if ( alch_counter == (numFepInitial + numFepFinal) ) break; |
| } | } |
| LJAvgA1 = sumOfAs1 / count1; | LJAvgA1 = sumOfAs1 / count1; |