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Update Colvars library to version 2019-04-26

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The following is list of relevant issues fixed and improvements:

Fix forces and missing output of runtime histogram for histogramRestraint
https://github.com/Colvars/colvars/pull/246

Use fix_modify to add configuration to Colvars:
https://github.com/Colvars/colvars/pull/216

Fix componentCoeff and name not working with orientationAngle components:
https://github.com/Colvars/colvars/issues/213

Fix 1-timestep offset with extendedLagrangian:
https://github.com/Colvars/colvars/pull/210

Changes to improve compiler support:
https://github.com/Colvars/colvars/pull/203

Fix ignored anisotropic cutoff3 for groupCoordNum:
https://github.com/Colvars/colvars/pull/202

New dipoleMagnitude variable:
https://github.com/Colvars/colvars/pull/198

Parser improvements:
https://github.com/Colvars/colvars/pull/196
This commit is contained in:
Giacomo Fiorin
2019-04-30 09:50:12 -04:00
parent 0005ee3e93
commit 7e00acce53
45 changed files with 2378 additions and 1328 deletions
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8
lib/colvars/colvarvalue.cpp
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@ -144,10 +144,10 @@ void colvarvalue::apply_constraints()
case colvarvalue::type_quaternionderiv:
break;
case colvarvalue::type_unit3vector:
rvector_value /= std::sqrt(rvector_value.norm2());
rvector_value /= cvm::sqrt(rvector_value.norm2());
break;
case colvarvalue::type_quaternion:
quaternion_value /= std::sqrt(quaternion_value.norm2());
quaternion_value /= cvm::sqrt(quaternion_value.norm2());
break;
case colvarvalue::type_vector:
if (elem_types.size() > 0) {
@ -579,7 +579,7 @@ colvarvalue colvarvalue::dist2_grad(colvarvalue const &x2) const
cvm::rvector const &v1 = this->rvector_value;
cvm::rvector const &v2 = x2.rvector_value;
cvm::real const cos_t = v1 * v2;
cvm::real const sin_t = std::sqrt(1.0 - cos_t*cos_t);
cvm::real const sin_t = cvm::sqrt(1.0 - cos_t*cos_t);
return colvarvalue( 2.0 * sin_t *
cvm::rvector((-1.0) * sin_t * v2.x +
cos_t/sin_t * (v1.x - cos_t*v2.x),
@ -630,7 +630,7 @@ colvarvalue const colvarvalue::interpolate(colvarvalue const &x1,
break;
case colvarvalue::type_unit3vector:
case colvarvalue::type_quaternion:
if (interp.norm()/std::sqrt(d2) < 1.0e-6) {
if (interp.norm()/cvm::sqrt(d2) < 1.0e-6) {
cvm::error("Error: interpolation between "+cvm::to_str(x1)+" and "+
cvm::to_str(x2)+" with lambda = "+cvm::to_str(lambda)+
" is undefined: result = "+cvm::to_str(interp)+"\n",