Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F79180974
colvarvalue.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sun, Aug 25, 03:59
Size
18 KB
Mime Type
text/x-c
Expires
Tue, Aug 27, 03:59 (2 d)
Engine
blob
Format
Raw Data
Handle
20160297
Attached To
rLAMMPS lammps
colvarvalue.cpp
View Options
// -*- c++ -*-
#include <vector>
#include <sstream>
#include <iostream>
#include "colvarmodule.h"
#include "colvarvalue.h"
void colvarvalue::add_elem(colvarvalue const &x)
{
if (this->value_type != type_vector) {
cvm::error("Error: trying to set an element for a variable that is not set to be a vector.\n");
return;
}
size_t const n = vector1d_value.size();
size_t const nd = num_dimensions(x.value_type);
elem_types.push_back(x.value_type);
elem_indices.push_back(n);
elem_sizes.push_back(nd);
vector1d_value.resize(n + nd);
set_elem(n, x);
}
colvarvalue const colvarvalue::get_elem(int const i_begin, int const i_end, Type const vt) const
{
if (vector1d_value.size() > 0) {
cvm::vector1d<cvm::real> const v(vector1d_value.slice(i_begin, i_end));
return colvarvalue(v, vt);
} else {
cvm::error("Error: trying to get an element from a variable that is not a vector.\n");
return colvarvalue(type_notset);
}
}
void colvarvalue::set_elem(int const i_begin, int const i_end, colvarvalue const &x)
{
if (vector1d_value.size() > 0) {
vector1d_value.sliceassign(i_begin, i_end, x.as_vector());
} else {
cvm::error("Error: trying to set an element for a variable that is not a vector.\n");
}
}
colvarvalue const colvarvalue::get_elem(int const icv) const
{
if (elem_types.size() > 0) {
return get_elem(elem_indices[icv], elem_indices[icv] + elem_sizes[icv],
elem_types[icv]);
} else {
cvm::error("Error: trying to get a colvarvalue element from a vector colvarvalue that was initialized as a plain array.\n");
return colvarvalue(type_notset);
}
}
void colvarvalue::set_elem(int const icv, colvarvalue const &x)
{
if (elem_types.size() > 0) {
check_types_assign(elem_types[icv], x.value_type);
set_elem(elem_indices[icv], elem_indices[icv] + elem_sizes[icv], x);
} else {
cvm::error("Error: trying to set a colvarvalue element for a colvarvalue that was initialized as a plain array.\n");
}
}
colvarvalue colvarvalue::inverse() const
{
switch (value_type) {
case colvarvalue::type_scalar:
return colvarvalue(1.0/real_value);
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return colvarvalue(cvm::rvector(1.0/rvector_value.x,
1.0/rvector_value.y,
1.0/rvector_value.z));
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return colvarvalue(cvm::quaternion(1.0/quaternion_value.q0,
1.0/quaternion_value.q1,
1.0/quaternion_value.q2,
1.0/quaternion_value.q3));
break;
case colvarvalue::type_vector:
{
cvm::vector1d<cvm::real> result(vector1d_value);
if (elem_types.size() > 0) {
// if we have information about non-scalar types, use it
size_t i;
for (i = 0; i < elem_types.size(); i++) {
result.sliceassign(elem_indices[i], elem_indices[i]+elem_sizes[i],
cvm::vector1d<cvm::real>((this->get_elem(i)).inverse()));
}
} else {
size_t i;
for (i = 0; i < result.size(); i++) {
if (result[i] != 0.0) {
result = 1.0/result[i];
}
}
}
return colvarvalue(result, type_vector);
}
break;
case colvarvalue::type_notset:
default:
undef_op();
break;
}
return colvarvalue();
}
// binary operations between two colvarvalues
colvarvalue operator + (colvarvalue const &x1,
colvarvalue const &x2)
{
colvarvalue::check_types(x1, x2);
switch (x1.value_type) {
case colvarvalue::type_scalar:
return colvarvalue(x1.real_value + x2.real_value);
case colvarvalue::type_3vector:
return colvarvalue(x1.rvector_value + x2.rvector_value);
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return colvarvalue(x1.rvector_value + x2.rvector_value,
colvarvalue::type_unit3vector);
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return colvarvalue(x1.quaternion_value + x2.quaternion_value);
case colvarvalue::type_vector:
return colvarvalue(x1.vector1d_value + x2.vector1d_value, colvarvalue::type_vector);
case colvarvalue::type_notset:
default:
x1.undef_op();
return colvarvalue(colvarvalue::type_notset);
};
}
colvarvalue operator - (colvarvalue const &x1,
colvarvalue const &x2)
{
colvarvalue::check_types(x1, x2);
switch (x1.value_type) {
case colvarvalue::type_scalar:
return colvarvalue(x1.real_value - x2.real_value);
case colvarvalue::type_3vector:
return colvarvalue(x1.rvector_value - x2.rvector_value);
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return colvarvalue(x1.rvector_value - x2.rvector_value,
colvarvalue::type_unit3vector);
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return colvarvalue(x1.quaternion_value - x2.quaternion_value);
case colvarvalue::type_vector:
return colvarvalue(x1.vector1d_value - x2.vector1d_value, colvarvalue::type_vector);
case colvarvalue::type_notset:
default:
x1.undef_op();
return colvarvalue(colvarvalue::type_notset);
};
}
// binary operations with real numbers
colvarvalue operator * (cvm::real const &a,
colvarvalue const &x)
{
switch (x.value_type) {
case colvarvalue::type_scalar:
return colvarvalue(a * x.real_value);
case colvarvalue::type_3vector:
return colvarvalue(a * x.rvector_value);
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return colvarvalue(a * x.rvector_value,
colvarvalue::type_unit3vector);
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return colvarvalue(a * x.quaternion_value);
case colvarvalue::type_vector:
return colvarvalue(x.vector1d_value * a, colvarvalue::type_vector);
case colvarvalue::type_notset:
default:
x.undef_op();
return colvarvalue(colvarvalue::type_notset);
}
}
colvarvalue operator * (colvarvalue const &x,
cvm::real const &a)
{
return a * x;
}
colvarvalue operator / (colvarvalue const &x,
cvm::real const &a)
{
switch (x.value_type) {
case colvarvalue::type_scalar:
return colvarvalue(x.real_value / a);
case colvarvalue::type_3vector:
return colvarvalue(x.rvector_value / a);
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return colvarvalue(x.rvector_value / a,
colvarvalue::type_unit3vector);
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return colvarvalue(x.quaternion_value / a);
case colvarvalue::type_vector:
return colvarvalue(x.vector1d_value / a, colvarvalue::type_vector);
case colvarvalue::type_notset:
default:
x.undef_op();
return colvarvalue(colvarvalue::type_notset);
}
}
// inner product between two colvarvalues
cvm::real operator * (colvarvalue const &x1,
colvarvalue const &x2)
{
colvarvalue::check_types(x1, x2);
switch (x1.value_type) {
case colvarvalue::type_scalar:
return (x1.real_value * x2.real_value);
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return (x1.rvector_value * x2.rvector_value);
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
// the "*" product is the quaternion product, here the inner
// member function is used instead
return (x1.quaternion_value.inner(x2.quaternion_value));
case colvarvalue::type_vector:
return (x1.vector1d_value * x2.vector1d_value);
case colvarvalue::type_notset:
default:
x1.undef_op();
return 0.0;
};
}
colvarvalue colvarvalue::dist2_grad(colvarvalue const &x2) const
{
colvarvalue::check_types(*this, x2);
switch (this->value_type) {
case colvarvalue::type_scalar:
return 2.0 * (this->real_value - x2.real_value);
case colvarvalue::type_3vector:
return 2.0 * (this->rvector_value - x2.rvector_value);
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
{
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);
return colvarvalue( 2.0 * sin_t *
cvm::rvector((-1.0) * sin_t * v2.x +
cos_t/sin_t * (v1.x - cos_t*v2.x),
(-1.0) * sin_t * v2.y +
cos_t/sin_t * (v1.y - cos_t*v2.y),
(-1.0) * sin_t * v2.z +
cos_t/sin_t * (v1.z - cos_t*v2.z)
),
colvarvalue::type_unit3vector );
}
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return this->quaternion_value.dist2_grad(x2.quaternion_value);
case colvarvalue::type_vector:
return colvarvalue(2.0 * (this->vector1d_value - x2.vector1d_value), colvarvalue::type_vector);
break;
case colvarvalue::type_notset:
default:
this->undef_op();
return colvarvalue(colvarvalue::type_notset);
};
}
std::string colvarvalue::to_simple_string() const
{
switch (type()) {
case colvarvalue::type_scalar:
return cvm::to_str(real_value, 0, cvm::cv_prec);
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return rvector_value.to_simple_string();
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return quaternion_value.to_simple_string();
break;
case colvarvalue::type_vector:
return vector1d_value.to_simple_string();
break;
case colvarvalue::type_notset:
default:
undef_op();
break;
}
return std::string();
}
int colvarvalue::from_simple_string(std::string const &s)
{
switch (type()) {
case colvarvalue::type_scalar:
return ((std::istringstream(s) >> real_value)
? COLVARS_OK : COLVARS_ERROR);
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return rvector_value.from_simple_string(s);
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return quaternion_value.from_simple_string(s);
break;
case colvarvalue::type_vector:
return vector1d_value.from_simple_string(s);
break;
case colvarvalue::type_notset:
default:
undef_op();
break;
}
return COLVARS_ERROR;
}
std::ostream & operator << (std::ostream &os, colvarvalue const &x)
{
switch (x.type()) {
case colvarvalue::type_scalar:
os << x.real_value;
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
os << x.rvector_value;
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
os << x.quaternion_value;
break;
case colvarvalue::type_vector:
os << x.vector1d_value;
break;
case colvarvalue::type_notset:
default:
os << "not set";
break;
}
return os;
}
std::ostream & operator << (std::ostream &os, std::vector<colvarvalue> const &v)
{
size_t i;
for (i = 0; i < v.size(); i++) {
os << v[i];
}
return os;
}
std::istream & operator >> (std::istream &is, colvarvalue &x)
{
if (x.type() == colvarvalue::type_notset) {
cvm::error("Trying to read from a stream a colvarvalue, "
"which has not yet been assigned a data type.\n");
return is;
}
switch (x.type()) {
case colvarvalue::type_scalar:
is >> x.real_value;
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vectorderiv:
is >> x.rvector_value;
break;
case colvarvalue::type_unit3vector:
is >> x.rvector_value;
x.apply_constraints();
break;
case colvarvalue::type_quaternion:
is >> x.quaternion_value;
x.apply_constraints();
break;
case colvarvalue::type_quaternionderiv:
is >> x.quaternion_value;
break;
case colvarvalue::type_vector:
is >> x.vector1d_value;
break;
case colvarvalue::type_notset:
default:
x.undef_op();
}
return is;
}
size_t colvarvalue::output_width(size_t const &real_width) const
{
switch (this->value_type) {
case colvarvalue::type_scalar:
return real_width;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return cvm::rvector::output_width(real_width);
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return cvm::quaternion::output_width(real_width);
case colvarvalue::type_vector:
// note how this depends on the vector's size
return vector1d_value.output_width(real_width);
case colvarvalue::type_notset:
default:
return 0;
}
}
void colvarvalue::inner_opt(colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &result)
{
// doing type check only once, here
colvarvalue::check_types(x, *xv);
std::vector<colvarvalue>::iterator &xvi = xv;
std::vector<cvm::real>::iterator &ii = result;
switch (x.value_type) {
case colvarvalue::type_scalar:
while (xvi != xv_end) {
*(ii++) += (xvi++)->real_value * x.real_value;
}
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
while (xvi != xv_end) {
*(ii++) += (xvi++)->rvector_value * x.rvector_value;
}
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
while (xvi != xv_end) {
*(ii++) += ((xvi++)->quaternion_value).cosine(x.quaternion_value);
}
break;
case colvarvalue::type_vector:
while (xvi != xv_end) {
*(ii++) += (xvi++)->vector1d_value * x.vector1d_value;
}
break;
default:
x.undef_op();
};
}
void colvarvalue::inner_opt(colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &result)
{
// doing type check only once, here
colvarvalue::check_types(x, *xv);
std::list<colvarvalue>::iterator &xvi = xv;
std::vector<cvm::real>::iterator &ii = result;
switch (x.value_type) {
case colvarvalue::type_scalar:
while (xvi != xv_end) {
*(ii++) += (xvi++)->real_value * x.real_value;
}
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
while (xvi != xv_end) {
*(ii++) += (xvi++)->rvector_value * x.rvector_value;
}
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
while (xvi != xv_end) {
*(ii++) += ((xvi++)->quaternion_value).cosine(x.quaternion_value);
}
break;
case colvarvalue::type_vector:
while (xvi != xv_end) {
*(ii++) += (xvi++)->vector1d_value * x.vector1d_value;
}
break;
default:
x.undef_op();
};
}
void colvarvalue::p2leg_opt(colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &result)
{
// doing type check only once, here
colvarvalue::check_types(x, *xv);
std::vector<colvarvalue>::iterator &xvi = xv;
std::vector<cvm::real>::iterator &ii = result;
switch (x.value_type) {
case colvarvalue::type_scalar:
cvm::error("Error: cannot calculate Legendre polynomials "
"for scalar variables.\n");
return;
break;
case colvarvalue::type_3vector:
while (xvi != xv_end) {
cvm::real const cosine =
((xvi)->rvector_value * x.rvector_value) /
((xvi)->rvector_value.norm() * x.rvector_value.norm());
xvi++;
*(ii++) += 1.5*cosine*cosine - 0.5;
}
break;
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
while (xvi != xv_end) {
cvm::real const cosine = (xvi++)->rvector_value * x.rvector_value;
*(ii++) += 1.5*cosine*cosine - 0.5;
}
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
while (xvi != xv_end) {
cvm::real const cosine = (xvi++)->quaternion_value.cosine(x.quaternion_value);
*(ii++) += 1.5*cosine*cosine - 0.5;
}
break;
case colvarvalue::type_vector:
while (xvi != xv_end) {
cvm::real const cosine =
((xvi)->vector1d_value * x.vector1d_value) /
((xvi)->vector1d_value.norm() * x.rvector_value.norm());
xvi++;
*(ii++) += 1.5*cosine*cosine - 0.5;
}
break;
default:
x.undef_op();
};
}
void colvarvalue::p2leg_opt(colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &result)
{
// doing type check only once, here
colvarvalue::check_types(x, *xv);
std::list<colvarvalue>::iterator &xvi = xv;
std::vector<cvm::real>::iterator &ii = result;
switch (x.value_type) {
case colvarvalue::type_scalar:
cvm::error("Error: cannot calculate Legendre polynomials "
"for scalar variables.\n");
break;
case colvarvalue::type_3vector:
while (xvi != xv_end) {
cvm::real const cosine =
((xvi)->rvector_value * x.rvector_value) /
((xvi)->rvector_value.norm() * x.rvector_value.norm());
xvi++;
*(ii++) += 1.5*cosine*cosine - 0.5;
}
break;
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
while (xvi != xv_end) {
cvm::real const cosine = (xvi++)->rvector_value * x.rvector_value;
*(ii++) += 1.5*cosine*cosine - 0.5;
}
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
while (xvi != xv_end) {
cvm::real const cosine = (xvi++)->quaternion_value.cosine(x.quaternion_value);
*(ii++) += 1.5*cosine*cosine - 0.5;
}
break;
default:
x.undef_op();
};
}
Event Timeline
Log In to Comment