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synchronize with the colvars git repo again

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This commit is contained in:
Axel Kohlmeyer
2014-10-22 10:38:06 -04:00
parent ff0d7028fe
commit c47c1428c2
7 changed files with 125 additions and 144 deletions
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103
lib/colvars/colvar.cpp
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@ -187,39 +187,19 @@ colvar::colvar (std::string const &conf)
for (j = 0; j < cvcs.size(); j++) {
sorted_cvc_values.push_back(cvcs[j]->p_value());
}
}
if (!tasks[task_scripted]) {
// this is set false if any of the components has an exponent
// different from 1 in the polynomial
b_linear = true;
// these will be set to false if any of the cvcs has them false
b_inverse_gradients = true;
b_Jacobian_force = true;
}
// Test whether this is a single-component variable
// Decide whether the colvar is periodic
// Used to wrap extended DOF if extendedLagrangian is on
if (cvcs.size() == 1 && (cvcs[0])->sup_np == 1
&& (cvcs[0])->sup_coeff == 1.0
&& !tasks[task_scripted]) {
b_single_cvc = true;
b_periodic = (cvcs[0])->b_periodic;
period = (cvcs[0])->period;
// TODO write explicit wrap() function for colvars to allow for
// sup_coeff different from 1
// this->period = (cvcs[0])->period * (cvcs[0])->sup_coeff;
} else {
b_single_cvc = false;
b_homogeneous = false;
// Scripted functions are deemed non-periodic
b_periodic = false;
period = 0.0;
b_inverse_gradients = false;
b_Jacobian_force = false;
}
// check the available features of each cvc
for (i = 0; i < cvcs.size(); i++) {
// check for linear combinations
b_linear = !tasks[task_scripted];
for (i = 0; i < cvcs.size(); i++) {
if ((cvcs[i])->b_debug_gradients)
enable (task_gradients);
@ -237,7 +217,41 @@ colvar::colvar (std::string const &conf)
(cvcs[i])->function_type+"\" approaches zero.\n");
}
}
}
// Colvar is homogeneous iff:
// - it is not scripted
// - it is linear
// - all cvcs have coefficient 1 or -1
// i.e. sum or difference of cvcs
b_homogeneous = !tasks[task_scripted] && b_linear;
for (i = 0; i < cvcs.size(); i++) {
if ((std::fabs(cvcs[i]->sup_coeff) - 1.0) > 1.0e-10) {
b_homogeneous = false;
}
}
// Colvar is deemed periodic iff:
// - it is homogeneous
// - all cvcs are periodic
// - all cvcs have the same period
b_periodic = cvcs[0]->b_periodic && b_homogeneous;
period = cvcs[0]->period;
for (i = 1; i < cvcs.size(); i++) {
if (!cvcs[i]->b_periodic || cvcs[i]->period != period) {
b_periodic = false;
period = 0.0;
}
}
// these will be set to false if any of the cvcs has them false
b_inverse_gradients = !tasks[task_scripted];
b_Jacobian_force = !tasks[task_scripted];
// check the available features of each cvc
for (i = 0; i < cvcs.size(); i++) {
if ((cvcs[i])->b_periodic && !b_periodic) {
cvm::log ("Warning: although this component is periodic, the colvar will "
"not be treated as periodic, either because the exponent is not "
@ -251,22 +265,17 @@ colvar::colvar (std::string const &conf)
if (! (cvcs[i])->b_Jacobian_derivative)
b_Jacobian_force = false;
if (!tasks[task_scripted]) {
// If the combination of components is a scripted function,
// the components may have different types
for (size_t j = i; j < cvcs.size(); j++) {
if ( (cvcs[i])->type() != (cvcs[j])->type() ) {
cvm::log ("ERROR: you are definining this collective variable "
"by using components of different types, \""+
colvarvalue::type_desc[(cvcs[i])->type()]+
"\" and \""+
colvarvalue::type_desc[(cvcs[j])->type()]+
"\". "
"You must use the same type in order to "
" sum them together.\n");
cvm::set_error_bits(INPUT_ERROR);
}
}
// components may have different types only for scripted functions
if (!tasks[task_scripted] && (cvcs[i])->type() != (cvcs[0])->type() ) {
cvm::error("ERROR: you are definining this collective variable "
"by using components of different types, \""+
colvarvalue::type_desc[(cvcs[0])->type()]+
"\" and \""+
colvarvalue::type_desc[(cvcs[i])->type()]+
"\". "
"You must use the same type in order to "
" sum them together.\n", INPUT_ERROR);
return;
}
}
@ -1235,7 +1244,7 @@ bool colvar::periodic_boundaries() const
cvm::real colvar::dist2 (colvarvalue const &x1,
colvarvalue const &x2) const
{
if (b_single_cvc) {
if (b_homogeneous) {
return (cvcs[0])->dist2(x1, x2);
} else {
return x1.dist2(x2);
@ -1245,7 +1254,7 @@ cvm::real colvar::dist2 (colvarvalue const &x1,
colvarvalue colvar::dist2_lgrad (colvarvalue const &x1,
colvarvalue const &x2) const
{
if (b_single_cvc) {
if (b_homogeneous) {
return (cvcs[0])->dist2_lgrad (x1, x2);
} else {
return x1.dist2_grad(x2);
@ -1255,7 +1264,7 @@ colvarvalue colvar::dist2_lgrad (colvarvalue const &x1,
colvarvalue colvar::dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const
{
if (b_single_cvc) {
if (b_homogeneous) {
return (cvcs[0])->dist2_rgrad (x1, x2);
} else {
return x2.dist2_grad(x1);
@ -1264,7 +1273,7 @@ colvarvalue colvar::dist2_rgrad (colvarvalue const &x1,
void colvar::wrap (colvarvalue &x) const
{
if (b_single_cvc) {
if (b_homogeneous) {
(cvcs[0])->wrap (x);
}
return;