Fixing bug in read_resume#1
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Line 1098 and 1102, fscanf followed by fgets does not properly account for newline character, results in erroneous read of number of sites (ns_tmp). Adding newline character results in accurate reading.
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Mar 11, 2026
…threshold Three bugs fixed: 1. d_MS_pair corruption: the previous code set MS_pair[j]=1 for all co-molecular particles then copied the modified array back to d_MS_pair. On the next CalcSTensors() call every head particle computed its u-vector toward particle rar-ensemble#1 instead of its actual bonded partner, producing garbage S tensors and NaN eigenvalues (Eigen assertion failure). Fix: use a local std::vector<int> dist_marker so this->MS_pair and d_MS_pair are never modified; restore d_MS_pair from this->MS_pair after the mapping kernel. 2. d_S_field not zeroed: d_mapDistributedFieldSTensors uses atomicAdd, so calling it without zeroing d_S_field first accumulated contributions from the preceding CalcSTensors() call. Fix: zero d_S_field with d_zero_float_vector before the mapping kernel. 3. Head-particle threshold: the condition was MS_pair[i] > 1, missing heads whose bonded partner has index 0 or 1. Fix: change to >= 0 (non-LC particles have MS_pair == -1). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Line 1098 and 1102, fscanf followed by fgets does not properly account for newline character, results in erroneous read of number of sites (ns_tmp). Adding newline character results in accurate reading.