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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12612 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-10-07 20:30:25 +00:00
parent 3c0612815f
commit 044084847b
33 changed files with 2284 additions and 2595 deletions
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18
lib/colvars/colvarcomp_angles.cpp
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@ -1,3 +1,4 @@
/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvar.h"
@ -6,7 +7,6 @@
#include <cmath>
colvar::angle::angle (std::string const &conf)
: cvc (conf)
{
@ -75,6 +75,7 @@ void colvar::angle::calc_value()
void colvar::angle::calc_gradients()
{
size_t i;
cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
cvm::real const dxdcos = -1.0 / std::sqrt (1.0 - cos_theta*cos_theta);
@ -84,17 +85,17 @@ void colvar::angle::calc_gradients()
dxdr3 = (180.0/PI) * dxdcos *
(1.0/r23l) * ( r21/r21l + (-1.0) * cos_theta * r23/r23l );
for (size_t i = 0; i < group1.size(); i++) {
for (i = 0; i < group1.size(); i++) {
group1[i].grad = (group1[i].mass/group1.total_mass) *
(dxdr1);
}
for (size_t i = 0; i < group2.size(); i++) {
for (i = 0; i < group2.size(); i++) {
group2[i].grad = (group2[i].mass/group2.total_mass) *
(dxdr1 + dxdr3) * (-1.0);
}
for (size_t i = 0; i < group3.size(); i++) {
for (i = 0; i < group3.size(); i++) {
group3[i].grad = (group3[i].mass/group3.total_mass) *
(dxdr3);
}
@ -307,16 +308,17 @@ void colvar::dihedral::calc_gradients()
+dsindB.y*r34.x - dsindB.x*r34.y);
}
for (size_t i = 0; i < group1.size(); i++)
size_t i;
for (i = 0; i < group1.size(); i++)
group1[i].grad = (group1[i].mass/group1.total_mass) * (-f1);
for (size_t i = 0; i < group2.size(); i++)
for (i = 0; i < group2.size(); i++)
group2[i].grad = (group2[i].mass/group2.total_mass) * (-f2 + f1);
for (size_t i = 0; i < group3.size(); i++)
for (i = 0; i < group3.size(); i++)
group3[i].grad = (group3[i].mass/group3.total_mass) * (-f3 + f2);
for (size_t i = 0; i < group4.size(); i++)
for (i = 0; i < group4.size(); i++)
group4[i].grad = (group4[i].mass/group4.total_mass) * (f3);
}