25#include "colvaratoms.h"
27#include "colvar_geometricpath.h"
104 cvc(std::string
const &conf);
115 virtual int init(std::string
const &conf);
124 char const *group_key,
125 bool optional =
false);
144 virtual const std::vector<feature *> &
features()
const
148 virtual std::vector<feature *> &modify_features()
152 static void delete_features() {
268 virtual int set_param(std::string
const ¶m_name,
void const *new_value);
775 angle(std::string
const &conf);
942 ef_anisotropic = (1<<8),
943 ef_use_pairlist = (1<<9),
944 ef_rebuild_pairlist = (1<<10)
961 bool **pairlist_elem,
968 template<
int flags>
void main_loop(
bool **pairlist_elem);
1063 h_bond(std::string
const &conf);
1145 std::vector<h_bond *>
hb;
1179 std::vector<dihedral *> theta;
1180 std::vector<cvm::real> coeffs;
1184 dihedPC(std::string
const &conf);
1231 std::unique_ptr<rotation_derivative_impl_> rot_deriv_impl;
1237 virtual int init(std::string
const &conf);
1261 virtual int init(std::string
const &conf);
1286 virtual int init(std::string
const &conf);
1312 tilt(std::string
const &conf);
1313 virtual int init(std::string
const &conf);
1341 virtual int init(std::string
const &conf);
1366 virtual int init(std::string
const &conf);
1388 virtual int init(std::string
const &conf);
1410 virtual int init(std::string
const &conf);
1538 cvm::error(
"Error: this component is not enabled in the current build; please see https://colvars.github.io/README-c++11.html");
1552 virtual void computeDistanceBetweenReferenceFrames(std::vector<cvm::real>& result);
1553 virtual void computeDistanceToReferenceFrames(std::vector<cvm::real>& result);
1560 std::vector<std::vector<cvm::atom_pos>> reference_fitting_frames;
1582 virtual void prepareVectors();
1583 virtual void updateDistanceToReferenceFrames();
1585 gspath(std::string
const &conf);
1604 virtual void prepareVectors();
1605 virtual void updateDistanceToReferenceFrames();
1607 gzpath(std::string
const &conf);
1620 std::vector<colvar::cvc*>
cv;
1624 cvm::real getPolynomialFactorOfCVGradient(
size_t i_cv)
const;
1639 bool use_custom_function;
1642 std::vector<Lepton::CompiledExpression *> value_evaluators;
1644 std::vector<Lepton::CompiledExpression *> gradient_evaluators;
1646 std::vector<double *> value_eval_var_refs;
1647 std::vector<double *> grad_eval_var_refs;
1665 std::vector<colvar::cvc*>
cv;
1667 std::vector<std::vector<colvarvalue>>
ref_cv;
1673 virtual void computeDistanceToReferenceFrames(std::vector<cvm::real>& result);
1676 cvm::real getPolynomialFactorOfCVGradient(
size_t i_cv)
const;
1693 virtual void updateDistanceToReferenceFrames();
1694 virtual void prepareVectors();
1709 virtual void updateDistanceToReferenceFrames();
1710 virtual void prepareVectors();
1725 std::unique_ptr<ArithmeticPathImpl> impl_;
1728 aspath(std::string
const &conf);
1739 std::unique_ptr<ArithmeticPathImpl> impl_;
1742 azpath(std::string
const &conf);
1753 std::unique_ptr<ArithmeticPathImpl> impl_;
1768 std::unique_ptr<ArithmeticPathImpl> impl_;
1779namespace neuralnetworkCV {
1780 class neuralNetworkCompute;
1789 std::unique_ptr<neuralnetworkCV::neuralNetworkCompute>
nn;
1811 virtual int init(std::string
const &conf);
1844#define simple_scalar_dist_functions(TYPE) \
1847 cvm::real colvar::TYPE::dist2(colvarvalue const &x1, \
1848 colvarvalue const &x2) const \
1850 return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
1854 colvarvalue colvar::TYPE::dist2_lgrad(colvarvalue const &x1, \
1855 colvarvalue const &x2) const \
1857 return 2.0 * (x1.real_value - x2.real_value); \
1861 colvarvalue colvar::TYPE::dist2_rgrad(colvarvalue const &x1, \
1862 colvarvalue const &x2) const \
1864 return this->dist2_lgrad(x2, x1); \
Definition: colvar_geometricpath.h:24
Definition: colvarcomp.h:1662
std::vector< colvar::cvc * > cv
Sub-colvar components.
Definition: colvarcomp.h:1665
size_t total_reference_frames
Total number of reference frames.
Definition: colvarcomp.h:1671
bool use_explicit_gradients
If all sub-cvs use explicit gradients then we also use it.
Definition: colvarcomp.h:1669
std::vector< std::vector< colvarvalue > > ref_cv
Reference colvar values from path.
Definition: colvarcomp.h:1667
virtual void calc_value()=0
Calculate the variable.
virtual void computeDistanceBetweenReferenceFrames(std::vector< cvm::real > &result) const
Helper function to determine the distance between reference frames.
Definition: colvarcomp_gpath.cpp:539
virtual void apply_force(colvarvalue const &force)=0
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp.h:1550
cvm::atom_group * atoms
Selected atoms.
Definition: colvarcomp.h:1555
std::vector< std::vector< cvm::atom_pos > > reference_frames
Reference frames.
Definition: colvarcomp.h:1559
virtual void apply_force(colvarvalue const &force)=0
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
size_t total_reference_frames
Total number of reference frames.
Definition: colvarcomp.h:1564
bool has_user_defined_fitting
Fitting options.
Definition: colvarcomp.h:1557
virtual void calc_value()=0
Calculate the variable.
std::vector< cvm::atom_group * > comp_atoms
Atom groups for RMSD calculation together with reference frames.
Definition: colvarcomp.h:1562
Definition: colvarcomp.h:1514
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:85
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:90
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:74
Definition: colvarcomp.h:1491
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:33
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_alchlambda.cpp:47
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:52
Colvar component: alpha helix content of a contiguous segment of 5 or more residues,...
Definition: colvarcomp.h:1132
void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_protein.cpp:176
cvm::real theta_tol
Tolerance on the Calpha-Calpha angle.
Definition: colvarcomp.h:1139
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:1136
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:187
void calc_value()
Calculate the variable.
Definition: colvarcomp_protein.cpp:132
cvm::real hb_coeff
Contribution of the hb terms.
Definition: colvarcomp.h:1148
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:239
std::vector< h_bond * > hb
List of hydrogen bonds.
Definition: colvarcomp.h:1145
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:1142
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:751
bool b_1site_force
Definition: colvarcomp.h:771
cvm::atom_group * group3
Atom group.
Definition: colvarcomp.h:759
cvm::rvector r21
Inter site vectors.
Definition: colvarcomp.h:762
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:757
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:766
cvm::real r21l
Inter site vector norms.
Definition: colvarcomp.h:764
cvm::atom_group * group1
Atom group.
Definition: colvarcomp.h:755
Definition: colvarcomp.h:1751
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_apath.cpp:249
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_apath.cpp:264
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_apath.cpp:288
Definition: colvarcomp.h:1723
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_apath.cpp:176
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_apath.cpp:167
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_apath.cpp:152
Definition: colvarcomp.h:1766
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_apath.cpp:358
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_apath.cpp:343
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_apath.cpp:382
Definition: colvarcomp.h:1737
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_apath.cpp:212
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_apath.cpp:221
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_apath.cpp:197
Definition: colvarcomp.h:1471
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:1550
cvm::atom_group * atoms
Atom group.
Definition: colvarcomp.h:1474
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:1538
std::vector< size_t > axes
Which Cartesian coordinates to include.
Definition: colvarcomp.h:1476
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:1558
Definition: colvarcomp.h:1535
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp.h:1541
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp.h:1542
virtual void apply_force(colvarvalue const &)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp.h:1543
Colvar component: coordination number between two groups (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:895
int en
Integer exponent of the function numerator.
Definition: colvarcomp.h:908
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:19
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_coordnums.cpp:270
int compute_coordnum()
Workhorse function.
Definition: colvarcomp_coordnums.cpp:221
cvm::atom_group * group2
Second atom group.
Definition: colvarcomp.h:900
cvm::real tolerance
Tolerance for the pair list.
Definition: colvarcomp.h:916
bool b_group2_center_only
If true, group2 will be treated as a single atom.
Definition: colvarcomp.h:913
int ed
Integer exponent of the function denominator.
Definition: colvarcomp.h:910
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_coordnums.cpp:281
int pairlist_freq
Frequency of update of the pair list.
Definition: colvarcomp.h:919
cvm::real r0
"Cutoff" for isotropic calculation (default)
Definition: colvarcomp.h:902
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:906
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:922
void main_loop(bool **pairlist_elem)
Workhorse function.
Definition: colvarcomp_coordnums.cpp:194
cvm::atom_group * group1
First atom group.
Definition: colvarcomp.h:898
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:287
cvm::rvector r0_vec
"Cutoff vector" for anisotropic calculation
Definition: colvarcomp.h:904
custom expression of colvars
Definition: colvarcomp.h:1637
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_combination.cpp:252
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_combination.cpp:290
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_combination.cpp:221
Colvar component (base class for collective variables)
Definition: colvarcomp.h:70
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:474
virtual int init_total_force_params(std::string const &conf)
Parse options pertaining to total force calculation.
Definition: colvarcomp.cpp:140
virtual void wrap(colvarvalue &x_unwrapped) const
Wrap value (for periodic/symmetric cvcs)
Definition: colvarcomp.cpp:680
void set_value(colvarvalue const &new_value)
Definition: colvarcomp.h:275
std::string function_type
Description of the type of collective variable.
Definition: colvarcomp.h:85
int sup_np
Exponent in the polynomial combination (default: 1)
Definition: colvarcomp.h:93
int set_function_type(std::string const &type)
Set the value of function_type and its dependencies.
Definition: colvarcomp.cpp:62
cvm::real sup_coeff
Coefficient in the polynomial combination (default: 1.0)
Definition: colvarcomp.h:91
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp.cpp:516
colvarvalue jd
Calculated Jacobian derivative (divergence of the inverse gradients): serves to calculate the phase s...
Definition: colvarcomp.h:301
std::vector< std::string > function_types
Record the type of this class as well as those it is derived from.
Definition: colvarcomp.h:285
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:673
virtual int init(std::string const &conf)
Definition: colvarcomp.cpp:83
virtual void debug_gradients()
Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component.
Definition: colvarcomp.cpp:540
virtual ~cvc()
Destructor.
Definition: colvarcomp.cpp:344
colvarvalue const & Jacobian_derivative() const
Return the previously calculated divergence of the inverse atomic gradients.
Definition: colvarcomp.h:338
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp.h:170
cvm::real width
CVC-specific default colvar width.
Definition: colvarcomp.h:322
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:666
virtual colvarvalue const * get_param_grad(std::string const ¶m_name)
Pointer to the gradient of parameter param_name.
Definition: colvarcomp.cpp:400
int setup()
After construction, set data related to dependency handling.
Definition: colvarcomp.cpp:337
virtual int set_param(std::string const ¶m_name, void const *new_value)
Set the named parameter to the given value.
Definition: colvarcomp.cpp:408
int init_code
Current initialization state; TODO remove this when using init() after default constructor.
Definition: colvarcomp.h:107
colvarvalue const & value() const
Return the previously calculated value.
Definition: colvarcomp.h:326
static std::vector< feature * > cvc_features
Implementation of the feature list for colvar.
Definition: colvarcomp.h:141
virtual int init_dependencies()
Initialize dependency tree.
Definition: colvarcomp.cpp:231
colvarvalue ft
Calculated total force (Note: this is calculated from the total atomic forces read from the program,...
Definition: colvarcomp.h:297
int update_description()
Update the description string based on name and type.
Definition: colvarcomp.cpp:46
std::string name
The name of the object (helps to identify this cvc instance when debugging)
Definition: colvarcomp.h:75
bool b_try_scalable
Whether or not this CVC will be computed in parallel whenever possible.
Definition: colvarcomp.h:271
cvm::real wrap_center
If the component is periodic, wrap around this value (default: 0.0)
Definition: colvarcomp.h:99
virtual void calc_value()=0
Calculate the variable.
virtual void read_data()
Obtain data needed for the calculation for the backend.
Definition: colvarcomp.cpp:434
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:659
colvarvalue x
Cached value.
Definition: colvarcomp.h:288
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp.cpp:524
void calc_fit_gradients()
Calculate the atomic fit gradients.
Definition: colvarcomp.cpp:532
void init_as_periodic_angle()
Set data types for a periodic angle (-180° to 180°)
Definition: colvarcomp.cpp:371
virtual std::vector< std::vector< int > > get_atom_lists()
Get vector of vectors of atom IDs for all atom groups.
Definition: colvarcomp.cpp:456
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:393
void init_as_angle()
Set data types for a bounded angle (0° to 180°)
Definition: colvarcomp.cpp:364
void init_as_distance()
Set data types for a scalar distance (convenience function)
Definition: colvarcomp.cpp:354
colvarvalue const & total_force() const
Return the previously calculated total force.
Definition: colvarcomp.h:332
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:291
colvarvalue upper_boundary
Location of the upper boundary (not defined by user choice)
Definition: colvarcomp.h:319
colvarvalue lower_boundary
Location of the lower boundary (not defined by user choice)
Definition: colvarcomp.h:316
void init_scalar_boundaries(cvm::real lb, cvm::real ub)
Set two scalar boundaries (convenience function)
Definition: colvarcomp.cpp:380
std::vector< cvm::atom_group * > atom_groups
Pointers to all atom groups, to let colvars collect info e.g. atomic gradients.
Definition: colvarcomp.h:259
std::string config_key
Keyword used in the input to denote this CVC.
Definition: colvarcomp.h:88
virtual const std::vector< feature * > & features() const
Implementation of the feature list accessor for colvar.
Definition: colvarcomp.h:144
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:170
cvm::real period
Period of the values of this CVC (default: 0.0, non periodic)
Definition: colvarcomp.h:96
Colvar component: dihedPC Projection of the config onto a dihedral principal component See e....
Definition: colvarcomp.h:1176
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:459
void calc_value()
Calculate the variable.
Definition: colvarcomp_protein.cpp:439
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:451
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:482
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:844
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:854
cvm::rvector r12
Inter site vectors.
Definition: colvarcomp.h:856
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:848
cvm::atom_group * group3
Atom group.
Definition: colvarcomp.h:852
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:860
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:850
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:798
bool b_1site_force
Definition: colvarcomp.h:818
cvm::rvector r21
Inter site vectors.
Definition: colvarcomp.h:809
cvm::real r21l
Inter site vector norms.
Definition: colvarcomp.h:811
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:813
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:802
cvm::atom_group * group3
Atom group.
Definition: colvarcomp.h:806
dipole_angle(std::string const &conf)
Initialize by parsing the configuration.
cvm::atom_group * group2
Atom group.
Definition: colvarcomp.h:804
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:607
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:789
cvm::atom_group * atoms
Dipole atom group.
Definition: colvarcomp.h:610
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:769
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:778
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:408
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to override the distance ones.
Definition: colvarcomp_distances.cpp:544
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:523
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:513
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to override the distance ones.
Definition: colvarcomp_distances.cpp:537
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:501
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to override the distance ones.
Definition: colvarcomp_distances.cpp:551
Colvar component: average distance between two groups of atoms, weighted as the sixth power,...
Definition: colvarcomp.h:559
cvm::atom_group * group2
Second atom group.
Definition: colvarcomp.h:564
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:644
int exponent
Components of the distance vector orthogonal to the axis.
Definition: colvarcomp.h:566
cvm::atom_group * group1
First atom group.
Definition: colvarcomp.h:562
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:595
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:639
Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type,...
Definition: colvarcomp.h:587
cvm::atom_group * group2
Second atom group.
Definition: colvarcomp.h:592
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:680
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:717
cvm::atom_group * group1
First atom group.
Definition: colvarcomp.h:590
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:711
Definition: colvarcomp.h:382
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the box periodicity.
Definition: colvarcomp_distances.cpp:162
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the box periodicity.
Definition: colvarcomp_distances.cpp:155
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:120
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the box periodicity.
Definition: colvarcomp_distances.cpp:148
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:131
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:138
Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:474
cvm::rvector dist_v_ortho
Components of the distance vector orthogonal to the axis.
Definition: colvarcomp.h:477
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:416
cvm::rvector v12
Vector distances.
Definition: colvarcomp.h:479
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:464
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:392
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:445
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:458
Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type,...
Definition: colvarcomp.h:433
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:260
cvm::rvector dist_v
Vector distance, cached to be recycled.
Definition: colvarcomp.h:446
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:343
cvm::atom_group * main
Main atom group.
Definition: colvarcomp.h:436
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to make use of the user-provided period.
Definition: colvarcomp_distances.cpp:355
bool fixed_axis
Flag: using a fixed axis vector?
Definition: colvarcomp.h:448
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:331
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:286
cvm::real axis_norm
Norm of the axis.
Definition: colvarcomp.h:444
cvm::atom_group * ref1
Reference atom group.
Definition: colvarcomp.h:438
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:319
cvm::atom_group * ref2
Optional, second ref atom group.
Definition: colvarcomp.h:440
cvm::rvector axis
Vector on which the distance vector is projected.
Definition: colvarcomp.h:442
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:230
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:305
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:299
Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:350
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:86
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:355
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:80
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:48
cvm::rvector dist_v
Vector distance, cached to be recycled.
Definition: colvarcomp.h:357
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:68
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:60
cvm::atom_group * group1
First atom group.
Definition: colvarcomp.h:353
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:712
std::vector< cvm::atom_pos > ref_pos
Reference coordinates.
Definition: colvarcomp.h:719
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:1433
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:1452
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:1416
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:722
cvm::atom_group * atoms
Atom group.
Definition: colvarcomp.h:716
cvm::real eigenvec_invnorm2
Inverse square norm of the eigenvector.
Definition: colvarcomp.h:725
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:1425
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:1440
Definition: colvarcomp.h:1362
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:523
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:564
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:573
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:555
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:582
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:506
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:498
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:546
Definition: colvarcomp.h:1384
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:683
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:617
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:642
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:701
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:665
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:625
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:692
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:674
Definition: colvarcomp.h:1406
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:759
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:791
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:736
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:782
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:807
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:799
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:744
Colvar component: coordination number between two groups (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:1018
cvm::rvector r0_vec
"Cutoff vector" for anisotropic calculation
Definition: colvarcomp.h:1023
bool b_anisotropic
Wheter dist/r0 or \vec{dist}*\vec{1/r0_vec} should ne be used.
Definition: colvarcomp.h:1026
int en
Integer exponent of the function numerator.
Definition: colvarcomp.h:1028
int ed
Integer exponent of the function denominator.
Definition: colvarcomp.h:1030
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:595
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:1021
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:644
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_coordnums.cpp:618
Colvar component: alternative path collective variable using geometry, variable s Allow any combinati...
Definition: colvarcomp.h:1691
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_gpath.cpp:650
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_gpath.cpp:681
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_gpath.cpp:645
Colvar component: alternative path collective variable using geometry, variable s For more informatio...
Definition: colvarcomp.h:1577
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_gpath.cpp:272
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_gpath.cpp:267
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_gpath.cpp:293
Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:637
cvm::atom_group * atoms
Atoms involved.
Definition: colvarcomp.h:640
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:821
virtual void calc_force_invgrads()
Calculate the total force from the system using the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:840
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:831
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:853
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:859
Definition: colvarcomp.h:1707
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_gpath.cpp:810
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_gpath.cpp:778
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_gpath.cpp:783
Colvar component: alternative path collective variable using geometry, variable z This should be merg...
Definition: colvarcomp.h:1598
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_gpath.cpp:410
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_gpath.cpp:415
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_gpath.cpp:426
Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang...
Definition: colvarcomp.h:1054
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:1061
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:387
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_coordnums.cpp:364
cvm::real r0
"Cutoff" distance between acceptor and donor
Definition: colvarcomp.h:1057
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:1059
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_coordnums.cpp:376
Colvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_sc...
Definition: colvarcomp.h:686
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:689
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:942
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_distances.cpp:924
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:934
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:663
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:878
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:895
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:887
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...
Current only linear combination of sub-CVCs is available.
Definition: colvarcomp.h:1617
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_combination.cpp:110
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_combination.cpp:80
std::vector< colvar::cvc * > cv
Sub-colvar components.
Definition: colvarcomp.h:1620
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_combination.cpp:94
bool use_explicit_gradients
If all sub-cvs use explicit gradients then we also use it.
Definition: colvarcomp.h:1622
Definition: colvarcomp.h:1805
std::string volmap_name
String identifier of the map object (as used by the simulation engine)
Definition: colvarcomp.h:1819
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_volmaps.cpp:103
int volmap_index
Index of the map objet in the proxy arrays.
Definition: colvarcomp.h:1825
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:133
cvm::atom_group * atoms
Group of atoms selected internally (optional)
Definition: colvarcomp.h:1828
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_volmaps.cpp:127
virtual int init(std::string const &conf)
Definition: colvarcomp_volmaps.cpp:40
std::vector< cvm::real > atom_weights
Weights assigned to each atom (default: uniform weights)
Definition: colvarcomp.h:1831
int volmap_id
Numeric identifier of the map object (as used by the simulation engine)
Definition: colvarcomp.h:1822
Definition: colvarcomp.h:1786
size_t m_output_index
the index of nn output components
Definition: colvarcomp.h:1791
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_neuralnetwork.cpp:142
std::unique_ptr< neuralnetworkCV::neuralNetworkCompute > nn
actual computation happens in neuralnetworkCV::neuralNetworkCompute
Definition: colvarcomp.h:1789
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_neuralnetwork.cpp:159
virtual void apply_force(colvarvalue const &force)
Apply the collective variable force, by communicating the atomic forces to the simulation program (No...
Definition: colvarcomp_neuralnetwork.cpp:176
Colvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type...
Definition: colvarcomp.h:1257
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:190
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:196
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:211
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:227
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:1281
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:251
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:278
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:257
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:266
Colvar component: orientation in space of an atom group, with respect to a set of reference coordinat...
Definition: colvarcomp.h:1208
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:141
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:158
cvm::rotation rot
Rotation object.
Definition: colvarcomp.h:1223
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:117
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:132
std::vector< cvm::atom_pos > shifted_pos
Shifted atomic positions.
Definition: colvarcomp.h:1220
cvm::atom_pos atoms_cog
Center of geometry of the group.
Definition: colvarcomp.h:1214
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:172
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:165
std::vector< cvm::atom_pos > ref_pos
Reference coordinates.
Definition: colvarcomp.h:1217
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:1227
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:38
cvm::atom_group * atoms
Atom group.
Definition: colvarcomp.h:1212
Colvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180])
Definition: colvarcomp.h:502
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:532
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:1432
size_t best_perm_index
Index of the permutation yielding the smallest RMSD (0 for identity)
Definition: colvarcomp.h:1446
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_distances.cpp:1116
virtual void calc_Jacobian_derivative()
Calculate the divergence of the inverse atomic gradients.
Definition: colvarcomp_distances.cpp:1151
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:1130
std::vector< cvm::atom_pos > ref_pos
Definition: colvarcomp.h:1440
cvm::atom_group * atoms
Atom group.
Definition: colvarcomp.h:1436
size_t n_permutations
Number of permutations of symmetry-related atoms.
Definition: colvarcomp.h:1443
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:1137
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:1089
Colvar component: self-coordination number within a group (colvarvalue::type_scalar type,...
Definition: colvarcomp.h:978
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:982
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_coordnums.cpp:523
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:529
int compute_selfcoordnum()
Main workhorse function.
Definition: colvarcomp_coordnums.cpp:450
int ed
Integer exponent of the function denominator.
Definition: colvarcomp.h:988
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_coordnums.cpp:512
cvm::real r0
"Cutoff" for isotropic calculation (default)
Definition: colvarcomp.h:984
int en
Integer exponent of the function numerator.
Definition: colvarcomp.h:986
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:1332
virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:436
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:426
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:398
virtual colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:445
virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:454
virtual int init(std::string const &conf)
Definition: colvarcomp_rotations.cpp:371
virtual void wrap(colvarvalue &x_unwrapped) const
Redefined to handle the 2*PI periodicity.
Definition: colvarcomp_rotations.cpp:463
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:410
Colvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scal...
Definition: colvarcomp.h:1305
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:346
virtual void calc_gradients()
Calculate the atomic gradients, to be reused later in order to apply forces.
Definition: colvarcomp_rotations.cpp:330
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:303
virtual void calc_value()
Calculate the variable.
Definition: colvarcomp_rotations.cpp:319
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:709
colvarvalue ft
Total force, as derived from the atomic trajectory; should equal the system force plus f.
Definition: colvar.h:222
std::vector< int > atom_ids
Sorted array of (zero-based) IDs for all atoms involved.
Definition: colvar.h:704
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:159
Stores numeric id, mass and all mutable data for an atom, mostly used by a colvar::cvc.
Definition: colvaratoms.h:31
1-dimensional vector of real numbers with four components and a quaternion algebra
Definition: colvartypes.h:958
A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion)
Definition: colvartypes.h:1314
vector of real numbers with three components
Definition: colvartypes.h:727
double real
Defining an abstract real number allows to switch precision.
Definition: colvarmodule.h:87
static int error(std::string const &message, int code=-1)
Print a message to the main log and set global error code.
Definition: colvarmodule.cpp:2011
Base class containing parsing functions; all objects which need to parse input inherit from this.
Definition: colvarparse.h:27
Value of a collective variable: this is a metatype which can be set at runtime. By default it is set ...
Definition: colvarvalue.h:43
Collective variables main module.
Definition: colvarcomp_apath.cpp:22
Definition: colvarcomp_rotations.cpp:17