25#include "colvaratoms.h"
26#include "colvar_arithmeticpath.h"
28#if (__cplusplus >= 201103L)
30#include "colvar_geometricpath.h"
112 cvc(std::string
const &conf);
120 virtual int init(std::string
const &conf);
129 char const *group_key,
130 bool optional =
false);
149 virtual const std::vector<feature *> &
features()
const
153 virtual std::vector<feature *> &modify_features()
157 static void delete_features() {
273 virtual int set_param(std::string
const ¶m_name,
void const *new_value);
777 angle(std::string
const &conf);
944 ef_anisotropic = (1<<8),
945 ef_use_pairlist = (1<<9),
946 ef_rebuild_pairlist = (1<<10)
963 bool **pairlist_elem,
970 template<
int flags>
void main_loop(
bool **pairlist_elem);
1065 h_bond(std::string
const &conf);
1147 std::vector<h_bond *>
hb;
1181 std::vector<dihedral *> theta;
1182 std::vector<cvm::real> coeffs;
1186 dihedPC(std::string
const &conf);
1232 virtual int init(std::string
const &conf);
1256 virtual int init(std::string
const &conf);
1281 virtual int init(std::string
const &conf);
1307 tilt(std::string
const &conf);
1308 virtual int init(std::string
const &conf);
1336 virtual int init(std::string
const &conf);
1361 virtual int init(std::string
const &conf);
1383 virtual int init(std::string
const &conf);
1405 virtual int init(std::string
const &conf);
1533 cvm::error(
"Error: this component is not enabled in the current build; please see https://colvars.github.io/README-c++11.html");
1543#if (__cplusplus >= 201103L)
1548 virtual void computeDistanceToReferenceFrames(std::vector<cvm::real>& result);
1552 bool has_user_defined_fitting;
1554 std::vector<std::vector<cvm::atom_pos>> reference_frames;
1555 std::vector<std::vector<cvm::atom_pos>> reference_fitting_frames;
1557 std::vector<cvm::atom_group*> comp_atoms;
1559 size_t total_reference_frames;
1561 CartesianBasedPath(std::string
const &conf);
1562 virtual ~CartesianBasedPath();
1577 virtual void prepareVectors();
1578 virtual void updateDistanceToReferenceFrames();
1580 gspath(std::string
const &conf);
1581 virtual ~gspath() {}
1599 virtual void prepareVectors();
1600 virtual void updateDistanceToReferenceFrames();
1602 gzpath(std::string
const &conf);
1603 virtual ~gzpath() {}
1615 std::vector<colvar::cvc*> cv;
1617 bool use_explicit_gradients;
1619 cvm::real getPolynomialFactorOfCVGradient(
size_t i_cv)
const;
1621 linearCombination(std::string
const &conf);
1622 virtual ~linearCombination();
1630class colvar::customColvar
1634 bool use_custom_function;
1637 std::vector<Lepton::CompiledExpression *> value_evaluators;
1639 std::vector<Lepton::CompiledExpression *> gradient_evaluators;
1641 std::vector<double *> value_eval_var_refs;
1642 std::vector<double *> grad_eval_var_refs;
1647 customColvar(std::string
const &conf);
1648 virtual ~customColvar();
1660 std::vector<colvar::cvc*> cv;
1662 std::vector<std::vector<colvarvalue>> ref_cv;
1664 bool use_explicit_gradients;
1666 size_t total_reference_frames;
1668 virtual void computeDistanceToReferenceFrames(std::vector<cvm::real>& result);
1670 virtual void computeDistanceBetweenReferenceFrames(std::vector<cvm::real>& result)
const;
1671 cvm::real getPolynomialFactorOfCVGradient(
size_t i_cv)
const;
1673 CVBasedPath(std::string
const &conf);
1674 virtual ~CVBasedPath();
1688 virtual void updateDistanceToReferenceFrames();
1689 virtual void prepareVectors();
1691 gspathCV(std::string
const &conf);
1692 virtual ~gspathCV();
1704 virtual void updateDistanceToReferenceFrames();
1705 virtual void prepareVectors();
1707 gzpathCV(std::string
const &conf);
1708 virtual ~gzpathCV();
1720 virtual void updateDistanceToReferenceFrames();
1722 aspathCV(std::string
const &conf);
1723 virtual ~aspathCV();
1734 virtual void updateDistanceToReferenceFrames();
1736 azpathCV(std::string
const &conf);
1737 virtual ~azpathCV();
1744namespace neuralnetworkCV {
1745 class neuralNetworkCompute;
1749 :
public linearCombination
1753 std::unique_ptr<neuralnetworkCV::neuralNetworkCompute> nn;
1755 size_t m_output_index;
1757 neuralNetwork(std::string
const &conf);
1758 virtual ~neuralNetwork();
1849 virtual int init(std::string
const &conf);
1882#define simple_scalar_dist_functions(TYPE) \
1885 cvm::real colvar::TYPE::dist2(colvarvalue const &x1, \
1886 colvarvalue const &x2) const \
1888 return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
1892 colvarvalue colvar::TYPE::dist2_lgrad(colvarvalue const &x1, \
1893 colvarvalue const &x2) const \
1895 return 2.0 * (x1.real_value - x2.real_value); \
1899 colvarvalue colvar::TYPE::dist2_rgrad(colvarvalue const &x1, \
1900 colvarvalue const &x2) const \
1902 return this->dist2_lgrad(x2, x1); \
Definition: colvar_arithmeticpath.h:18
Definition: colvar_geometricpath.h:23
Definition: colvarcomp.h:1782
Definition: colvarcomp.h:1775
Definition: colvarcomp.h:1509
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_alchlambda.cpp:86
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_alchlambda.cpp:91
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_alchlambda.cpp:75
Definition: colvarcomp.h:1486
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_alchlambda.cpp:34
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_alchlambda.cpp:48
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_alchlambda.cpp:53
Colvar component: alpha helix content of a contiguous segment of 5 or more residues,...
Definition: colvarcomp.h:1134
void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_protein.cpp:177
cvm::real theta_tol
Tolerance on the Calpha-Calpha angle.
Definition: colvarcomp.h:1141
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
cvm::real theta_ref
Reference Calpha-Calpha angle (default: 88 degrees)
Definition: colvarcomp.h:1138
void collect_gradients(std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients)
Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs.
Definition: colvarcomp_protein.cpp:188
void calc_value()
Calculate the variable.
Definition: colvarcomp_protein.cpp:133
cvm::real hb_coeff
Contribution of the hb terms.
Definition: colvarcomp.h:1150
void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_protein.cpp:240
std::vector< h_bond * > hb
List of hydrogen bonds.
Definition: colvarcomp.h:1147
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
std::vector< angle * > theta
List of Calpha-Calpha angles.
Definition: colvarcomp.h:1144
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:753
bool b_1site_force
Definition: colvarcomp.h:773
cvm::atom_group * group3
Atom group.
Definition: colvarcomp.h:761
cvm::rvector r21
Inter site vectors.
Definition: colvarcomp.h:764
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_angles.cpp:123
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_angles.cpp:74
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_angles.cpp:114
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
cvm::atom_group * group2
Atom group.
Definition: colvarcomp.h:759
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_angles.cpp:53
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_angles.cpp:91
cvm::rvector dxdr1
Derivatives wrt group centers of mass.
Definition: colvarcomp.h:768
cvm::real r21l
Inter site vector norms.
Definition: colvarcomp.h:766
cvm::atom_group * group1
Atom group.
Definition: colvarcomp.h:757
Definition: colvarcomp.h:1817
Definition: colvarcomp.h:1824
Definition: colvarcomp.h:1466
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:1554
cvm::atom_group * atoms
Atom group.
Definition: colvarcomp.h:1469
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:1542
std::vector< size_t > axes
Which Cartesian coordinates to include.
Definition: colvarcomp.h:1471
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:1562
Definition: colvarcomp.h:1530
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp.h:1536
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp.h:1537
virtual void apply_force(colvarvalue const &)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp.h:1538
Colvar component: coordination number between two groups (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:897
int en
Integer exponent of the function numerator.
Definition: colvarcomp.h:910
static cvm::real switching_function(cvm::real const &r0, cvm::rvector const &r0_vec, int en, int ed, cvm::atom &A1, cvm::atom &A2, bool **pairlist_elem, cvm::real tolerance)
Calculate a coordination number through the function (1-x**n)/(1-x**m), where x = |A1-A2|/r0.
Definition: colvarcomp_coordnums.cpp:20
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_coordnums.cpp:271
int compute_coordnum()
Workhorse function.
Definition: colvarcomp_coordnums.cpp:222
cvm::atom_group * group2
Second atom group.
Definition: colvarcomp.h:902
cvm::real tolerance
Tolerance for the pair list.
Definition: colvarcomp.h:918
bool b_group2_center_only
If true, group2 will be treated as a single atom.
Definition: colvarcomp.h:915
int ed
Integer exponent of the function denominator.
Definition: colvarcomp.h:912
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_coordnums.cpp:282
int pairlist_freq
Frequency of update of the pair list.
Definition: colvarcomp.h:921
cvm::real r0
"Cutoff" for isotropic calculation (default)
Definition: colvarcomp.h:904
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
bool b_anisotropic
Whether r/r0 or \vec{r}*\vec{1/r0_vec} should be used.
Definition: colvarcomp.h:908
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
bool * pairlist
Pair list.
Definition: colvarcomp.h:924
void main_loop(bool **pairlist_elem)
Workhorse function.
Definition: colvarcomp_coordnums.cpp:195
cvm::atom_group * group1
First atom group.
Definition: colvarcomp.h:900
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_coordnums.cpp:288
cvm::rvector r0_vec
"Cutoff vector" for anisotropic calculation
Definition: colvarcomp.h:906
Colvar component (base class for collective variables)
Definition: colvarcomp.h:78
virtual void collect_gradients(std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients)
Calculate atomic gradients and add them to the corresponding item in gradient vector May be overridde...
Definition: colvarcomp.cpp:452
virtual int init_total_force_params(std::string const &conf)
Parse options pertaining to total force calculation.
Definition: colvarcomp.cpp:126
virtual void wrap(colvarvalue &x_unwrapped) const
Wrap value (for periodic/symmetric cvcs)
Definition: colvarcomp.cpp:658
void set_value(colvarvalue const &new_value)
Definition: colvarcomp.h:280
std::string function_type
Description of the type of collective variable.
Definition: colvarcomp.h:93
int sup_np
Exponent in the polynomial combination (default: 1)
Definition: colvarcomp.h:101
int set_function_type(std::string const &type)
Set the value of function_type and its dependencies.
Definition: colvarcomp.cpp:46
cvm::real sup_coeff
Coefficient in the polynomial combination (default: 1.0)
Definition: colvarcomp.h:99
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp.cpp:494
colvarvalue jd
Calculated Jacobian derivative (divergence of the inverse gradients): serves to calculate the phase s...
Definition: colvarcomp.h:303
std::vector< std::string > function_types
Record the type of this class as well as those it is derived from.
Definition: colvarcomp.h:287
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp.cpp:651
virtual int init(std::string const &conf)
Definition: colvarcomp.cpp:65
virtual void debug_gradients()
Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component.
Definition: colvarcomp.cpp:518
virtual ~cvc()
Destructor.
Definition: colvarcomp.cpp:322
colvarvalue const & Jacobian_derivative() const
Return the previously calculated divergence of the inverse atomic gradients.
Definition: colvarcomp.h:340
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp.h:175
cvm::real width
CVC-specific default colvar width.
Definition: colvarcomp.h:324
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp.cpp:644
virtual colvarvalue const * get_param_grad(std::string const ¶m_name)
Pointer to the gradient of parameter param_name.
Definition: colvarcomp.cpp:378
int setup()
After construction, set data related to dependency handling.
Definition: colvarcomp.cpp:315
virtual int set_param(std::string const ¶m_name, void const *new_value)
Set the named parameter to the given value.
Definition: colvarcomp.cpp:386
colvarvalue const & value() const
Return the previously calculated value.
Definition: colvarcomp.h:328
static std::vector< feature * > cvc_features
Implementation of the feature list for colvar.
Definition: colvarcomp.h:146
virtual int init_dependencies()
Initialize dependency tree.
Definition: colvarcomp.cpp:209
colvarvalue ft
Calculated total force (Note: this is calculated from the total atomic forces read from the program,...
Definition: colvarcomp.h:299
std::string name
The name of the object (helps to identify this cvc instance when debugging)
Definition: colvarcomp.h:83
bool b_try_scalable
Whether or not this CVC will be computed in parallel whenever possible.
Definition: colvarcomp.h:276
cvm::real wrap_center
If the component is periodic, wrap around this value (default: 0.0)
Definition: colvarcomp.h:107
virtual void calc_value()=0
Calculate the variable.
virtual void read_data()
Obtain data needed for the calculation for the backend.
Definition: colvarcomp.cpp:412
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
Definition: colvarcomp.cpp:637
colvarvalue x
Cached value.
Definition: colvarcomp.h:290
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp.cpp:502
void calc_fit_gradients()
Calculate the atomic fit gradients.
Definition: colvarcomp.cpp:510
void init_as_periodic_angle()
Set data types for a periodic angle (-180° to 180°)
Definition: colvarcomp.cpp:349
virtual std::vector< std::vector< int > > get_atom_lists()
Get vector of vectors of atom IDs for all atom groups.
Definition: colvarcomp.cpp:434
cvc()
Default constructor (used when colvar::cvc objects are declared within other ones)
Definition: colvarcomp.cpp:19
void register_atom_group(cvm::atom_group *ag)
Store a pointer to new atom group, and list as child for dependencies.
Definition: colvarcomp.cpp:371
void init_as_angle()
Set data types for a bounded angle (0° to 180°)
Definition: colvarcomp.cpp:342
void init_as_distance()
Set data types for a scalar distance (convenience function)
Definition: colvarcomp.cpp:332
colvarvalue const & total_force() const
Return the previously calculated total force.
Definition: colvarcomp.h:334
virtual void apply_force(colvarvalue const &cvforce)=0
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
colvarvalue x_old
Value at the previous step.
Definition: colvarcomp.h:293
colvarvalue upper_boundary
Location of the upper boundary (not defined by user choice)
Definition: colvarcomp.h:321
colvarvalue lower_boundary
Location of the lower boundary (not defined by user choice)
Definition: colvarcomp.h:318
void init_scalar_boundaries(cvm::real lb, cvm::real ub)
Set two scalar boundaries (convenience function)
Definition: colvarcomp.cpp:358
std::vector< cvm::atom_group * > atom_groups
Pointers to all atom groups, to let colvars collect info e.g. atomic gradients.
Definition: colvarcomp.h:264
std::string config_key
Keyword used in the input to denote this CVC.
Definition: colvarcomp.h:96
virtual const std::vector< feature * > & features() const
Implementation of the feature list accessor for colvar.
Definition: colvarcomp.h:149
cvm::atom_group * parse_group(std::string const &conf, char const *group_key, bool optional=false)
Within the constructor, make a group parse its own options from the provided configuration string Ret...
Definition: colvarcomp.cpp:156
cvm::real period
Period of the values of this CVC (default: 0.0, non periodic)
Definition: colvarcomp.h:104
Colvar component: dihedPC Projection of the config onto a dihedral principal component See e....
Definition: colvarcomp.h:1178
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
void collect_gradients(std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients)
Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs.
Definition: colvarcomp_protein.cpp:460
void calc_value()
Calculate the variable.
Definition: colvarcomp_protein.cpp:440
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_protein.cpp:452
void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_protein.cpp:483
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:846
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_angles.cpp:330
cvm::atom_group * group4
Atom group.
Definition: colvarcomp.h:856
cvm::rvector r12
Inter site vectors.
Definition: colvarcomp.h:858
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_angles.cpp:404
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_angles.cpp:435
cvm::atom_group * group1
Atom group.
Definition: colvarcomp.h:850
cvm::atom_group * group3
Atom group.
Definition: colvarcomp.h:854
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_angles.cpp:478
bool b_1site_force
Compute total force on first site only to avoid unwanted coupling to other colvars (see e....
Definition: colvarcomp.h:862
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_angles.cpp:487
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_angles.cpp:460
cvm::atom_group * group2
Atom group.
Definition: colvarcomp.h:852
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_angles.cpp:469
dihedral(std::string const &conf)
Initialize by parsing the configuration.
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_angles.cpp:301
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_angles.cpp:442
Colvar component: angle between the dipole of a molecule and an axis formed by two groups of atoms(co...
Definition: colvarcomp.h:800
bool b_1site_force
Definition: colvarcomp.h:820
cvm::rvector r21
Inter site vectors.
Definition: colvarcomp.h:811
cvm::real r21l
Inter site vector norms.
Definition: colvarcomp.h:813
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_angles.cpp:177
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_angles.cpp:232
cvm::rvector dxdr1
Derivatives wrt group centers of mass.
Definition: colvarcomp.h:815
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
cvm::atom_group * group1
Dipole atom group.
Definition: colvarcomp.h:804
cvm::atom_group * group3
Atom group.
Definition: colvarcomp.h:808
dipole_angle(std::string const &conf)
Initialize by parsing the configuration.
cvm::atom_group * group2
Atom group.
Definition: colvarcomp.h:806
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_angles.cpp:201
Colvar component: dipole magnitude of a molecule.
Definition: colvarcomp.h:609
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:790
cvm::atom_group * atoms
Dipole atom group.
Definition: colvarcomp.h:612
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:770
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:779
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Colvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue...
Definition: colvarcomp.h:410
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to override the distance ones.
Definition: colvarcomp_distances.cpp:545
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:524
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:514
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to override the distance ones.
Definition: colvarcomp_distances.cpp:538
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:502
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to override the distance ones.
Definition: colvarcomp_distances.cpp:552
Colvar component: average distance between two groups of atoms, weighted as the sixth power,...
Definition: colvarcomp.h:561
cvm::atom_group * group2
Second atom group.
Definition: colvarcomp.h:566
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:645
int exponent
Components of the distance vector orthogonal to the axis.
Definition: colvarcomp.h:568
cvm::atom_group * group1
First atom group.
Definition: colvarcomp.h:564
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:596
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:640
Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type,...
Definition: colvarcomp.h:589
cvm::atom_group * group2
Second atom group.
Definition: colvarcomp.h:594
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:681
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:718
cvm::atom_group * group1
First atom group.
Definition: colvarcomp.h:592
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:712
Definition: colvarcomp.h:384
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the box periodicity.
Definition: colvarcomp_distances.cpp:163
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the box periodicity.
Definition: colvarcomp_distances.cpp:156
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:121
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the box periodicity.
Definition: colvarcomp_distances.cpp:149
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:132
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:139
Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:476
cvm::rvector dist_v_ortho
Components of the distance vector orthogonal to the axis.
Definition: colvarcomp.h:479
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:417
cvm::rvector v12
Vector distances.
Definition: colvarcomp.h:481
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:465
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:393
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:446
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:459
Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type,...
Definition: colvarcomp.h:435
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:261
cvm::rvector dist_v
Vector distance, cached to be recycled.
Definition: colvarcomp.h:448
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_distances.cpp:344
cvm::atom_group * main
Main atom group.
Definition: colvarcomp.h:438
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to make use of the user-provided period.
Definition: colvarcomp_distances.cpp:356
bool fixed_axis
Flag: using a fixed axis vector?
Definition: colvarcomp.h:450
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_distances.cpp:332
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:287
cvm::real axis_norm
Norm of the axis.
Definition: colvarcomp.h:446
cvm::atom_group * ref1
Reference atom group.
Definition: colvarcomp.h:440
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
Definition: colvarcomp_distances.cpp:320
cvm::atom_group * ref2
Optional, second ref atom group.
Definition: colvarcomp.h:442
cvm::rvector axis
Vector on which the distance vector is projected.
Definition: colvarcomp.h:444
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:231
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:306
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:300
Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:352
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:87
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
cvm::atom_group * group2
Second atom group.
Definition: colvarcomp.h:357
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:81
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:49
cvm::rvector dist_v
Vector distance, cached to be recycled.
Definition: colvarcomp.h:359
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:69
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:61
cvm::atom_group * group1
First atom group.
Definition: colvarcomp.h:355
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
Colvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type,...
Definition: colvarcomp.h:714
std::vector< cvm::atom_pos > ref_pos
Reference coordinates.
Definition: colvarcomp.h:721
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:1439
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:1458
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:1422
eigenvector(std::string const &conf)
Constructor.
std::vector< cvm::rvector > eigenvec
Eigenvector (of a normal or essential mode): will always have zero center.
Definition: colvarcomp.h:724
cvm::atom_group * atoms
Atom group.
Definition: colvarcomp.h:718
cvm::real eigenvec_invnorm2
Inverse square norm of the eigenvector.
Definition: colvarcomp.h:727
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:1431
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:1446
Definition: colvarcomp.h:1357
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:491
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_rotations.cpp:529
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_rotations.cpp:538
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
Definition: colvarcomp_rotations.cpp:520
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:547
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:475
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:467
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_rotations.cpp:511
Definition: colvarcomp.h:1379
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_rotations.cpp:644
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:582
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:606
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:662
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_rotations.cpp:626
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:590
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_rotations.cpp:653
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
Definition: colvarcomp_rotations.cpp:635
Definition: colvarcomp.h:1401
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:719
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
Definition: colvarcomp_rotations.cpp:748
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:697
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_rotations.cpp:739
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_rotations.cpp:764
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_rotations.cpp:756
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:705
Colvar component: coordination number between two groups (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:1020
cvm::rvector r0_vec
"Cutoff vector" for anisotropic calculation
Definition: colvarcomp.h:1025
bool b_anisotropic
Wheter dist/r0 or \vec{dist}*\vec{1/r0_vec} should ne be used.
Definition: colvarcomp.h:1028
int en
Integer exponent of the function numerator.
Definition: colvarcomp.h:1030
int ed
Integer exponent of the function denominator.
Definition: colvarcomp.h:1032
groupcoordnum(std::string const &conf)
Constructor.
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_coordnums.cpp:596
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
cvm::real r0
"Cutoff" for isotropic calculation (default)
Definition: colvarcomp.h:1023
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_coordnums.cpp:645
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_coordnums.cpp:619
Definition: colvarcomp.h:1803
Definition: colvarcomp.h:1789
Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:639
cvm::atom_group * atoms
Atoms involved.
Definition: colvarcomp.h:642
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:822
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:841
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:832
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:854
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:860
Definition: colvarcomp.h:1810
Definition: colvarcomp.h:1796
Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang...
Definition: colvarcomp.h:1056
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
int ed
Integer exponent of the function denominator.
Definition: colvarcomp.h:1063
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_coordnums.cpp:388
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_coordnums.cpp:365
cvm::real r0
"Cutoff" distance between acceptor and donor
Definition: colvarcomp.h:1059
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
int en
Integer exponent of the function numerator.
Definition: colvarcomp.h:1061
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_coordnums.cpp:377
Colvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_sc...
Definition: colvarcomp.h:688
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
inertia_z(std::string const &conf)
Constructor.
cvm::rvector axis
Vector on which the inertia tensor is projected.
Definition: colvarcomp.h:691
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:943
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:925
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:935
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
Colvar component: moment of inertia of an atom group (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:665
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:879
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:896
inertia(std::string const &conf)
Constructor.
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:888
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp.h:1768
Definition: colvarcomp.h:1843
std::string volmap_name
String identifier of the map object (as used by the simulation engine)
Definition: colvarcomp.h:1857
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_volmaps.cpp:104
int volmap_index
Index of the map objet in the proxy arrays.
Definition: colvarcomp.h:1863
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_volmaps.cpp:134
cvm::atom_group * atoms
Group of atoms selected internally (optional)
Definition: colvarcomp.h:1866
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_volmaps.cpp:128
virtual int init(std::string const &conf)
Definition: colvarcomp_volmaps.cpp:41
std::vector< cvm::real > atom_weights
Weights assigned to each atom (default: uniform weights)
Definition: colvarcomp.h:1869
int volmap_id
Numeric identifier of the map object (as used by the simulation engine)
Definition: colvarcomp.h:1860
Definition: colvarcomp.h:1831
Colvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type...
Definition: colvarcomp.h:1252
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:175
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:181
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:195
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_rotations.cpp:208
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Colvar component: cosine of the angle of rotation with respect to a set of reference coordinates (col...
Definition: colvarcomp.h:1276
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:232
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_rotations.cpp:255
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:238
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:246
Colvar component: orientation in space of an atom group, with respect to a set of reference coordinat...
Definition: colvarcomp.h:1210
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_rotations.cpp:129
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
Definition: colvarcomp_rotations.cpp:143
cvm::rotation rot
Rotation object.
Definition: colvarcomp.h:1222
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:105
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:120
cvm::atom_pos atoms_cog
Center of geometry of the group.
Definition: colvarcomp.h:1216
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_rotations.cpp:157
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Definition: colvarcomp_rotations.cpp:150
std::vector< cvm::atom_pos > ref_pos
Reference coordinates.
Definition: colvarcomp.h:1219
cvm::quaternion ref_quat
This is used to remove jumps in the sign of the quaternion, which may be annoying in the colvars traj...
Definition: colvarcomp.h:1226
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:28
cvm::atom_group * atoms
Atom group.
Definition: colvarcomp.h:1214
Colvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180])
Definition: colvarcomp.h:504
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_angles.cpp:601
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_angles.cpp:592
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_angles.cpp:572
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_angles.cpp:619
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_angles.cpp:610
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_angles.cpp:628
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_angles.cpp:583
Colvar component: polar coordinate theta of a group (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:534
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to override the distance ones.
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to override the distance ones.
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to override the distance ones.
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_angles.cpp:543
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_angles.cpp:520
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_angles.cpp:531
Colvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coo...
Definition: colvarcomp.h:1427
size_t best_perm_index
Index of the permutation yielding the smallest RMSD (0 for identity)
Definition: colvarcomp.h:1441
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:1121
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:1156
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_distances.cpp:1135
std::vector< cvm::atom_pos > ref_pos
Definition: colvarcomp.h:1435
cvm::atom_group * atoms
Atom group.
Definition: colvarcomp.h:1431
size_t n_permutations
Number of permutations of symmetry-related atoms.
Definition: colvarcomp.h:1438
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:1142
rmsd(std::string const &conf)
Constructor.
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:1094
Colvar component: self-coordination number within a group (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:980
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
cvm::atom_group * group1
Selected atoms.
Definition: colvarcomp.h:984
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_coordnums.cpp:524
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_coordnums.cpp:530
int compute_selfcoordnum()
Main workhorse function.
Definition: colvarcomp_coordnums.cpp:451
int ed
Integer exponent of the function denominator.
Definition: colvarcomp.h:990
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_coordnums.cpp:513
cvm::real r0
"Cutoff" for isotropic calculation (default)
Definition: colvarcomp.h:986
int en
Integer exponent of the function numerator.
Definition: colvarcomp.h:988
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
Colvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:1327
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:405
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_rotations.cpp:395
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:371
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:414
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:423
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:344
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:432
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:382
Colvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scal...
Definition: colvarcomp.h:1300
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_rotations.cpp:319
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:306
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x1) of the square distance (can be redefined to transparently implement cons...
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:280
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:296
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Gradient(with respect to x2) of the square distance (can be redefined to transparently implement cons...
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Square distance between x1 and x2 (can be redefined to transparently implement constraints,...
std::vector< cvm::rvector > atomic_gradients
Array of atomic gradients collected from all cvcs with appropriate components, rotations etc....
Definition: colvar.h:690
colvarvalue ft
Total force, as derived from the atomic trajectory; should equal the system force plus f.
Definition: colvar.h:224
std::vector< int > atom_ids
Sorted array of (zero-based) IDs for all atoms involved.
Definition: colvar.h:685
Parent class for a member object of a bias, cv or cvc etc. containing features and their dependencies...
Definition: colvardeps.h:34
Group of atom objects, mostly used by a colvar::cvc object to gather all atomic data.
Definition: colvaratoms.h:156
Stores numeric id, mass and all mutable data for an atom, mostly used by a colvar::cvc.
Definition: colvaratoms.h:28
1-dimensional vector of real numbers with four components and a quaternion algebra
Definition: colvartypes.h:937
A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion)
Definition: colvartypes.h:1285
vector of real numbers with three components
Definition: colvartypes.h:703
double real
Defining an abstract real number allows to switch precision.
Definition: colvarmodule.h:100
static int error(std::string const &message, int code=COLVARS_ERROR)
Print a message to the main log and set global error code.
Definition: colvarmodule.cpp:1811
Base class containing parsing functions; all objects which need to parse input inherit from this.
Definition: colvarparse.h:26
Value of a collective variable: this is a metatype which can be set at runtime. By default it is set ...
Definition: colvarvalue.h:41
Collective variables main module.