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Update Colvars to version 2020-07-07

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This update contains several fixes and small new features or usability
improvements.  Descriptions and authorship information can be accessed from
the pull requests listed below.

Skip the zero-step also when multiple run commands are executed in sequence (@giacomofiorin)
https://github.com/Colvars/colvars/pull/357

Do not accumulate data at step 0 (@giacomofiorin)
https://github.com/Colvars/colvars/pull/345

Support for symmetry permutations of atoms in RMSD (@jhenin)
https://github.com/Colvars/colvars/pull/344

Detect new grid parameters (@jhenin)
https://github.com/Colvars/colvars/pull/341

Only access the output streams in non-threaded regions (@giacomofiorin)
https://github.com/Colvars/colvars/pull/338

Fix incomplete setting of default colvarsRestartFrequency (@giacomofiorin)
https://github.com/Colvars/colvars/pull/334

Fix typo (@e-kwsm)
https://github.com/Colvars/colvars/pull/333

Convert the input keyword to lowercase in read_state_data_key (@HanatoK)
https://github.com/Colvars/colvars/pull/332

Implement reflecting b.c. for ext Lagrangian (@jhenin)
https://github.com/Colvars/colvars/pull/329
This commit is contained in:
Giacomo Fiorin
2020-09-04 14:46:27 -04:00
parent d995ed0d87
commit 85c394453c
45 changed files with 3238 additions and 1582 deletions
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9
lib/colvars/colvar_UIestimator.h
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@ -116,7 +116,7 @@ namespace UIestimator {
int i;
for (i = 0; i < dimension; i++) {
temp[i] = round((round(y[i] / width[i] + EPSILON) - round(x[i] / width[i] + EPSILON)) + (y_size - 1) / 2 + EPSILON);
temp[i] = int(round((round(y[i] / width[i] + EPSILON) - round(x[i] / width[i] + EPSILON)) + (y_size - 1) / 2 + EPSILON));
}
int index = 0;
@ -305,12 +305,6 @@ namespace UIestimator {
int i;
if (step % output_freq == 0) {
calc_pmf();
write_files();
//write_interal_data();
}
for (i = 0; i < dimension; i++) {
// for dihedral RC, it is possible that x = 179 and y = -179, should correct it
// may have problem, need to fix
@ -381,6 +375,7 @@ namespace UIestimator {
bool written;
bool written_1D;
public:
// calculate gradients from the internal variables
void calc_pmf() {
int norm;