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lammps/lib/colvars/colvarvalue.cpp
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colvarvalue.cpp
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/// -*- 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();
};
}
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