15#include "colvars_version.h"
18#define COLVARS_DEBUG false
21#if defined(__FAST_MATH__)
23#define COLVARS_BOUNDED_INV_TRIGONOMETRIC_FUNC
26#define COLVARS_USE_SOA
50#if defined(COLVARS_CUDA)
51#include <cuda_runtime.h>
54#if defined(COLVARS_HIP)
55#include <hip/hip_runtime.h>
56#define cudaHostAllocMapped hipHostMallocMapped
57#define cudaHostAlloc hipHostMalloc
58#define cudaFreeHost hipHostFree
59#define cudaSuccess hipSuccess
85 return std::string(COLVARS_VERSION);
100#if ( defined(COLVARS_CUDA) || defined(COLVARS_HIP) )
101 template <
typename T>
102 class CudaHostAllocator {
104 using value_type = T;
106 CudaHostAllocator() =
default;
109 constexpr CudaHostAllocator(
const CudaHostAllocator<U>&)
noexcept {}
111 friend bool operator==(
const CudaHostAllocator&,
const CudaHostAllocator&) {
return true; }
112 friend bool operator!=(
const CudaHostAllocator&,
const CudaHostAllocator&) {
return false; }
114 T* allocate(
size_t n) {
116 if (cudaHostAlloc(&ptr, n *
sizeof(T), cudaHostAllocMapped) != cudaSuccess) {
117 throw std::bad_alloc();
121 void deallocate(T* ptr,
size_t n)
noexcept {
124 template<
typename U,
typename... Args>
125 void construct(U* p, Args&&... args) {
126 new(p) U(std::forward<Args>(args)...);
130 void destroy(U* p)
noexcept {
160 if (x == 0.0)
return 0.0;
161 int nn = (n > 0) ? n : -n;
163 for (yy = 1.0; nn != 0; nn >>= 1, ww *=ww) {
164 if (nn & 1) yy *= ww;
166 return (n > 0) ? yy : 1.0/yy;
172 return ::pow(
static_cast<double>(x),
static_cast<double>(y));
178 return ::floor(
static_cast<double>(x));
184 return ::fabs(
static_cast<double>(x));
190 return ::sqrt(
static_cast<double>(x));
196 return ::sin(
static_cast<double>(x));
202 return ::cos(
static_cast<double>(x));
206#define PI 3.14159265358979323846
209#define PI_2 1.57079632679489661923
215#ifdef COLVARS_BOUNDED_INV_TRIGONOMETRIC_FUNC
218 }
else if (x >= 1.0) {
221 return ::asin(
static_cast<double>(x));
224 return ::asin(
static_cast<double>(x));
231#ifdef COLVARS_BOUNDED_INV_TRIGONOMETRIC_FUNC
234 }
else if (x >= 1.0) {
237 return ::acos(
static_cast<double>(x));
240 return ::acos(
static_cast<double>(x));
247 return ::atan2(
static_cast<double>(x),
static_cast<double>(y));
253 return ::exp(
static_cast<double>(x));
261 return ::log(
static_cast<double>(x));
266 template <
class T>
class vector1d;
267 template <
class T>
class matrix2d;
287 typedef std::vector<atom>::iterator atom_iter;
288 typedef std::vector<atom>::const_iterator atom_const_iter;
298 static void set_error_bits(
int code);
300 static bool get_error_bit(
int code);
302 static inline int get_error()
307 static void clear_error();
366 void register_named_atom_group_soa(atom_group *ag);
367 void unregister_named_atom_group_soa(atom_group *ag);
416 return COLVARS_DEBUG;
460 static std::istream &
getline(std::istream &is, std::string &line);
492 template <
class bias_type>
545 template <
typename IST> IST & read_state_template_(IST &is);
577 template <
typename OST> OST &write_state_template_(OST &os);
655 long traj_read_begin,
659 static std::string
to_str(
char const *s);
662 static std::string
to_str(std::string
const &s);
665 static std::string
to_str(
bool x);
668 static std::string
to_str(
int const &x,
669 size_t width = 0,
size_t prec = 0);
672 static std::string
to_str(
size_t const &x,
673 size_t width = 0,
size_t prec = 0);
676 static std::string
to_str(
long int const &x,
677 size_t width = 0,
size_t prec = 0);
681 size_t width = 0,
size_t prec = 0);
685 size_t width = 0,
size_t prec = 0);
689 size_t width = 0,
size_t prec = 0);
693 size_t width = 0,
size_t prec = 0);
697 size_t width = 0,
size_t prec = 0);
701 size_t width = 0,
size_t prec = 0);
705 size_t width = 0,
size_t prec = 0);
709 static std::string
to_str(std::vector<int>
const &x,
710 size_t width = 0,
size_t prec = 0);
713 static std::string
to_str(std::vector<size_t>
const &x,
714 size_t width = 0,
size_t prec = 0);
717 static std::string
to_str(std::vector<long int>
const &x,
718 size_t width = 0,
size_t prec = 0);
721 static std::string
to_str(std::vector<real>
const &x,
722 size_t width = 0,
size_t prec = 0);
725 static std::string
to_str(std::vector<rvector>
const &x,
726 size_t width = 0,
size_t prec = 0);
729 static std::string
to_str(std::vector<quaternion>
const &x,
730 size_t width = 0,
size_t prec = 0);
733 static std::string
to_str(std::vector<colvarvalue>
const &x,
734 size_t width = 0,
size_t prec = 0);
737 static std::string
to_str(std::vector<std::string>
const &x,
738 size_t width = 0,
size_t prec = 0);
740#if ( defined(COLVARS_CUDA) || defined(COLVARS_HIP) )
741 static std::string
to_str(std::vector<
rvector, CudaHostAllocator<rvector>>
const &x,
742 size_t width = 0,
size_t prec = 0);
743 static std::string
to_str(std::vector<
real, CudaHostAllocator<real>>
const &x,
744 size_t width = 0,
size_t prec = 0);
783 static void log(std::string
const &message,
int min_log_level = 10);
786 static int error(std::string
const &message,
int code = -1);
860 std::vector<rvector> *pos,
862 std::string
const &pdb_field,
863 double pdb_field_value = 0.0);
867 std::vector<rvector> *pos,
869 bool keep_open =
false);
926 static size_t &
depth();
934 static inline bool scripted_forces()
963std::ostream & operator << (std::ostream &os,
cvm::rvector const &v);
964std::istream & operator >> (std::istream &is,
cvm::rvector &v);
968 constexpr int32_t COLVARS_OK = 0;
969 constexpr int32_t COLVARS_ERROR = 1;
970 constexpr int32_t COLVARS_NOT_IMPLEMENTED = (1<<1);
971 constexpr int32_t COLVARS_INPUT_ERROR = (1<<2);
972 constexpr int32_t COLVARS_BUG_ERROR = (1<<3);
973 constexpr int32_t COLVARS_FILE_ERROR = (1<<4);
974 constexpr int32_t COLVARS_MEMORY_ERROR = (1<<5);
975 constexpr int32_t COLVARS_NO_SUCH_FRAME = (1<<6);
A collective variable (main class); to be defined, it needs at least one object of a derived class of...
Definition: colvar.h:53
Collective variable bias, base class.
Definition: colvarbias.h:23
Arbitrary size array (two dimensions) suitable for linear algebra operations (i.e....
Definition: colvartypes.h:372
1-dimensional vector of real numbers with four components and a quaternion algebra
Definition: colvartypes.h:954
2-dimensional array of real numbers with three components along each dimension (works with colvarmodu...
Definition: colvartypes.h:891
vector of real numbers with three components
Definition: colvartypes.h:723
Track usage of Colvars features.
Definition: colvarmodule.cpp:35
Arbitrary size array (one dimensions) suitable for linear algebra operations (i.e....
Definition: colvartypes.h:33
Collective variables module (main class)
Definition: colvarmodule.h:78
int cite_feature(std::string const &feature)
Track usage of the given Colvars feature.
Definition: colvarmodule.cpp:2554
static const char *const line_marker
Line separator in the log output.
Definition: colvarmodule.h:763
rvector atom_pos
Atom position (different type name from rvector, to make possible future PBC-transparent implementati...
Definition: colvarmodule.h:279
int write_traj_files()
Write all trajectory files.
Definition: colvarmodule.cpp:1205
int load_coords_xyz(char const *filename, std::vector< rvector > *pos, atom_group *atoms, bool keep_open=false)
Load coordinates into an atom group from an XYZ file (assumes Angstroms)
std::ostream & write_state(std::ostream &os)
Write the state of the module to a formatted (text) file.
Definition: colvarmodule.cpp:1913
static std::string state_file_prefix(char const *filename)
Strips .colvars.state from filename and checks that it is not empty.
Definition: colvarmodule.cpp:1543
static real pow(real const &x, real const &y)
Reimplemented to work around MS compiler issues.
Definition: colvarmodule.h:170
size_t num_biases_feature(int feature_id) const
Return how many biases have this feature enabled.
Definition: colvarmodule.cpp:684
static real asin(real const &x)
Reimplemented to work around compiler issues; return hard-coded values for boundary conditions.
Definition: colvarmodule.h:213
static step_number it
Current step number.
Definition: colvarmodule.h:310
bool cv_traj_write_labels
Write labels at the next iteration.
Definition: colvarmodule.h:891
static std::string to_str(std::vector< quaternion > const &x, size_t width=0, size_t prec=0)
Convert to string for output purposes.
std::vector< std::string > const time_dependent_biases() const
Definition: colvarmodule.cpp:712
std::string cv_traj_name
Name of the trajectory file.
Definition: colvarmodule.h:888
static real logn(real const &x)
Definition: colvarmodule.h:259
std::ostream & write_traj(std::ostream &os)
Write in the trajectory file.
Definition: colvarmodule.cpp:1963
double real
Defining an abstract real number allows to switch precision.
Definition: colvarmodule.h:150
static size_t const en_prec
Number of digits to represent the collective variables energy.
Definition: colvarmodule.h:759
int read_config_string(std::string const &conf)
Parse a config string assuming it is a complete configuration (i.e. calling all parse functions)
Definition: colvarmodule.cpp:267
static std::string to_str(std::vector< rvector > const &x, size_t width=0, size_t prec=0)
Convert to string for output purposes.
static real floor(real const &x)
Reimplemented to work around MS compiler issues.
Definition: colvarmodule.h:176
static std::string wrap_string(std::string const &s, size_t nchars)
Reduce the number of characters in a string.
size_t size() const
How many objects (variables and biases) are configured yet?
Definition: colvarmodule.cpp:225
int xyz_reader_use_count
Track how many times the XYZ reader has been used.
Definition: colvarmodule.h:906
std::vector< std::string > index_group_names
Names of groups from one or more Gromacs .ndx files.
Definition: colvarmodule.h:840
usage * usage_
Track usage of Colvars features.
Definition: colvarmodule.h:909
int update_colvar_forces()
Integrate bias and restraint forces, send colvar forces to atoms.
Definition: colvarmodule.cpp:1085
std::string restart_version() const
Version of the most recent state file read.
Definition: colvarmodule.h:914
int set_input_state_buffer(size_t n, unsigned char *buf)
Set an internal state buffer, to be read later as an unformatted stream when ready.
Definition: colvarmodule.cpp:1647
int parse_config(std::string &conf)
Parse a "clean" config string (no comments)
Definition: colvarmodule.cpp:306
int write_restart_file(std::string const &out_name)
Write a state file useful to resume the simulation.
Definition: colvarmodule.cpp:1164
static void request_total_force()
Request calculation of total force from MD engine.
void set_initial_step(step_number it)
Set the initial step number (it is 0 otherwise); may be overridden when reading a state.
Definition: colvarmodule.cpp:231
static real exp(real const &x)
Reimplemented to work around MS compiler issues.
Definition: colvarmodule.h:251
memory_stream & read_state(memory_stream &is)
Read all objects' state fron an unformatted (binary) stream.
std::vector< int > * variables_active_smp_items()
Indexes of the items to calculate for each colvar.
Definition: colvarmodule.cpp:199
int residue_id
Residue identifier.
Definition: colvarmodule.h:275
std::vector< colvarbias * > biases_active_
Array of active collective variable biases.
Definition: colvarmodule.h:406
static int log_output_files()
Level at which output-file operations are logged.
Definition: colvarmodule.h:820
int end_of_step()
Carry out operations needed before next step is run.
Definition: colvarmodule.cpp:1278
size_t num_biases() const
Return how many biases are defined.
Definition: colvarmodule.cpp:678
int setup_output()
(Re)initialize the output trajectory and state file (does not write it yet)
Definition: colvarmodule.cpp:1498
bool check_new_bias(std::string &conf, char const *key)
Definition: colvarmodule.cpp:533
std::string feature_report(int flag=0)
Report usage of the Colvars features.
Definition: colvarmodule.cpp:2559
std::vector< int > colvars_smp_items
Indexes of the items to calculate for each colvar.
Definition: colvarmodule.h:359
static int load_coords(char const *filename, std::vector< rvector > *pos, atom_group *atoms, std::string const &pdb_field, double pdb_field_value=0.0)
Load coordinates for a group of atoms from a file (PDB or XYZ); if "pos" is already allocated,...
static int backup_file(char const *filename)
Backup a file before writing it.
Definition: colvarmodule.cpp:1771
int calc()
Main worker function.
Definition: colvarmodule.cpp:845
static real cos(real const &x)
Reimplemented to work around MS compiler issues.
Definition: colvarmodule.h:200
int patch_version_number() const
Get the patch version number (non-zero in patch releases of other packages)
Definition: colvarmodule.h:95
std::string extra_conf
Definition: colvarmodule.h:489
static real dt()
Time step of MD integrator (fs)
static step_number it_restart
Starting step number for this run.
Definition: colvarmodule.h:312
static real integer_power(real const &x, int const n)
Override the STL pow() with a product for n integer.
Definition: colvarmodule.h:156
std::string config_string
Configuration string read so far by the module (includes comments)
Definition: colvarmodule.h:485
std::string default_input_state_file_
Default input state file; if given, it is read unless the MD engine provides it.
Definition: colvarmodule.h:548
int read_config_file(char const *config_file_name)
Definition: colvarmodule.cpp:238
std::vector< std::vector< int > * > index_groups
Groups from one or more Gromacs .ndx files.
Definition: colvarmodule.h:843
int restart_version_number() const
Integer version of the most recent state file read.
Definition: colvarmodule.h:920
static atom_group * atom_group_soa_by_name(std::string const &name)
Look up a named atom group by name; returns NULL if not found.
Definition: colvarmodule.cpp:767
void * num_biases_types_used_
Pointer to a map counting how many biases of each type were used.
Definition: colvarmodule.h:403
int catch_input_errors(int result)
Useful wrapper to interrupt parsing if any error occurs.
Definition: colvarmodule.cpp:728
std::vector< std::string > index_file_names
Names of .ndx files that have been loaded.
Definition: colvarmodule.h:837
static int log_level_
Level of logging requested by the user.
Definition: colvarmodule.h:791
std::vector< colvar * > * variables_active()
Collective variables with the active flag on.
Definition: colvarmodule.cpp:187
std::vector< colvarbias * > * biases_active()
Array of active collective variable biases.
Definition: colvarmodule.cpp:219
int patch_version_int
Patch version number (non-zero in patch releases of other packages)
Definition: colvarmodule.h:142
int append_new_config(std::string const &conf)
Add new configuration during parsing (e.g. to implement back-compatibility); cannot be nested,...
Definition: colvarmodule.cpp:368
std::istream & read_objects_state(std::istream &is)
Read the states of individual objects; allows for changes.
Definition: colvarmodule.cpp:1662
real total_bias_energy
Energy of built-in and scripted biases, summed per time-step.
Definition: colvarmodule.h:398
static rvector position_distance(atom_pos const &pos1, atom_pos const &pos2)
Get the distance between two atomic positions with pbcs handled correctly.
size_t num_biases_type(std::string const &type) const
Return how many biases of this type are defined.
Definition: colvarmodule.cpp:698
static size_t const it_width
Number of characters to represent a time step.
Definition: colvarmodule.h:753
static bool use_scripted_forces
Use scripted colvars forces?
Definition: colvarmodule.h:940
std::istream & read_state(std::istream &is)
Read all objects' state fron a formatted (text) stream.
Definition: colvarmodule.cpp:1621
static void log(std::string const &message, int min_log_level=10)
Definition: colvarmodule.cpp:1988
std::vector< unsigned char > input_state_buffer_
Internal state buffer, to be read as an unformatted stream.
Definition: colvarmodule.h:551
colvarparse * parse
Configuration file parser object.
Definition: colvarmodule.h:885
int calc_component_smp(int i)
Calculate the value of the specified component (to be called in a SMP loop)
Definition: colvarmodule.cpp:205
static size_t cv_traj_freq
Frequency for collective variables trajectory output.
Definition: colvarmodule.h:872
static size_t & depth()
Get the current object depth in the hierarchy.
Definition: colvarmodule.cpp:2018
static bool scripting_after_biases
Wait for all biases before calculating scripted forces?
Definition: colvarmodule.h:943
std::string const & get_config() const
Get the configuration string read so far (includes comments)
Definition: colvarmodule.cpp:362
static size_t restart_out_freq
Frequency for saving output restarts.
Definition: colvarmodule.h:875
int parse_colvars(std::string const &conf)
Parse and initialize collective variables.
Definition: colvarmodule.cpp:484
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:2065
static int errorCode
Definition: colvarmodule.h:294
std::vector< colvar * > colvars
Array of collective variables.
Definition: colvarmodule.h:350
static real atan2(real const &x, real const &y)
Reimplemented to work around MS compiler issues.
Definition: colvarmodule.h:245
std::vector< colvar * > * variables_active_smp()
Definition: colvarmodule.cpp:193
std::vector< atom_group * > named_atom_groups_soa
Array of named atom groups.
Definition: colvarmodule.h:362
static void increase_depth()
Increase the depth (number of indentations in the output)
Definition: colvarmodule.cpp:2004
static real rand_gaussian()
Pseudo-random number with Gaussian distribution.
colvarmodule()
Cannot initialize the main object without a proxy.
int write_output_files()
Write all other output files.
Definition: colvarmodule.cpp:1777
static size_t const cv_prec
Number of digits to represent a collective variables value(s)
Definition: colvarmodule.h:755
static colvarmodule * main()
Access the one instance of the Colvars module.
Definition: colvarmodule.cpp:175
int parse_biases_type(std::string const &conf, char const *keyword)
Parse and initialize collective variable biases of a specific type.
Definition: colvarmodule.cpp:547
static real sqrt(real const &x)
Reimplemented to work around MS compiler issues.
Definition: colvarmodule.h:188
std::string version() const
Get the version string (YYYY-MM-DD format)
Definition: colvarmodule.h:83
static int log_level()
Level of logging requested by the user.
Definition: colvarmodule.h:796
int version_int
Integer representing the version string (allows comparisons)
Definition: colvarmodule.h:139
std::ostream & write_traj_label(std::ostream &os)
Write explanatory labels in the trajectory file.
Definition: colvarmodule.cpp:1938
static real acos(real const &x)
Reimplemented to work around compiler issues; return hard-coded values for boundary conditions.
Definition: colvarmodule.h:229
int reset()
Actual function called by the destructor.
Definition: colvarmodule.cpp:1353
int calc_biases()
Calculate biases.
Definition: colvarmodule.cpp:1011
std::vector< colvar * > colvars_smp
Definition: colvarmodule.h:357
std::vector< colvar * > colvars_active
Array of collective variables.
Definition: colvarmodule.h:353
int analyze()
Perform analysis.
Definition: colvarmodule.cpp:1250
std::string read_colvar(std::string const &name)
Read a colvar value.
Definition: colvarmodule.cpp:812
size_t num_variables() const
Return how many variables are defined.
Definition: colvarmodule.cpp:658
std::string restart_out_name
Output restart file name.
Definition: colvarmodule.h:877
int version_number() const
Get the version number (higher = more recent)
Definition: colvarmodule.h:89
int read_traj(char const *traj_filename, long traj_read_begin, long traj_read_end)
Read a collective variable trajectory (post-processing only, not called at runtime)
Definition: colvarmodule.cpp:1797
static size_t const cv_width
Number of characters to represent a collective variables value(s)
Definition: colvarmodule.h:757
size_t depth_s
Counter for the current depth in the object hierarchy (useg e.g. in output)
Definition: colvarmodule.h:900
static bool debug()
Whether debug output should be enabled (compile-time option)
Definition: colvarmodule.h:414
int change_configuration(std::string const &bias_name, std::string const &conf)
Definition: colvarmodule.cpp:794
std::vector< colvarbias * > biases
Array of collective variable biases.
Definition: colvarmodule.h:395
std::string restart_version_str
Version of the most recent state file read.
Definition: colvarmodule.h:894
int restart_version_int
Integer version of the most recent state file read.
Definition: colvarmodule.h:897
int calc_scripted_forces()
Calculate the energy and forces of scripted biases.
Definition: colvarmodule.cpp:1146
std::string source_Tcl_script
Initialization Tcl script, user-provided.
Definition: colvarmodule.h:500
int write_restart_string(std::string &output)
Write the state into a string.
Definition: colvarmodule.cpp:1193
static std::istream & getline(std::istream &is, std::string &line)
Definition: colvarmodule.cpp:286
static int log_input_files()
Level at which input-file operations (configuration, state) are logged.
Definition: colvarmodule.h:826
int calc_colvars()
Calculate collective variables.
Definition: colvarmodule.cpp:913
static real fabs(real const &x)
Reimplemented to work around MS compiler issues.
Definition: colvarmodule.h:182
std::vector< colvar * > * variables()
Array of collective variables.
Definition: colvarmodule.cpp:181
static void decrease_depth()
Decrease the depth (number of indentations in the output)
Definition: colvarmodule.cpp:2010
int update_engine_parameters()
Definition: colvarmodule.cpp:1305
real energy_difference(std::string const &bias_name, std::string const &conf)
Definition: colvarmodule.cpp:828
static int log_default_params()
Level at which a keyword's default value is logged.
Definition: colvarmodule.h:814
memory_stream & write_state(memory_stream &os)
Write the state of the module to an unformatted (binary) file.
int reset_index_groups()
Clear the index groups loaded so far.
Definition: colvarmodule.cpp:2173
static int log_user_params()
Level at which a keyword's user-provided value is logged.
Definition: colvarmodule.h:808
int print_total_forces_errning(bool warn_total_forces)
If needed (old restart file), print the warning that cannot be ignored.
Definition: colvarmodule.cpp:1747
memory_stream & read_objects_state(memory_stream &is)
Read the states of individual objects; allows for changes.
static step_number step_relative()
Return the current step number from the beginning of this run.
Definition: colvarmodule.h:315
int read_index_file(char const *filename)
Read a Gromacs .ndx file.
size_t num_variables_feature(int feature_id) const
Return how many variables have this feature enabled.
Definition: colvarmodule.cpp:664
static real sin(real const &x)
Reimplemented to work around MS compiler issues.
Definition: colvarmodule.h:194
~colvarmodule()
Destructor.
Definition: colvarmodule.cpp:1324
static std::string & output_prefix()
Accessor for the above.
Definition: colvarmodule.h:341
void config_changed()
Signals to the module object that the configuration has changed.
Definition: colvarmodule.cpp:375
static colvarproxy * proxy
Pointer to the proxy object, used to retrieve atomic data from the hosting program; it is static in o...
Definition: colvarmodule.h:951
static std::string to_str(char const *s)
Convert to string for output purposes.
Definition: colvarmodule.cpp:2407
static step_number step_absolute()
Definition: colvarmodule.h:322
static colvar * colvar_by_name(std::string const &name)
Look up a colvar by name; returns NULL if not found.
Definition: colvarmodule.cpp:754
static int log_init_messages()
Level at which initialization messages are logged.
Definition: colvarmodule.h:802
static colvarbias * bias_by_name(std::string const &name)
Look up a bias by name; returns NULL if not found.
Definition: colvarmodule.cpp:740
int open_traj_file(std::string const &file_name)
Open a trajectory file if requested (and leave it open)
std::string cvm_output_prefix
Prefix for all output files for this run.
Definition: colvarmodule.h:337
int setup_input()
(Re)initialize and (re)read the input state file calling read_restart()
Definition: colvarmodule.cpp:1388
int parse_biases(std::string const &conf)
Parse and initialize collective variable biases.
Definition: colvarmodule.cpp:591
int write_state_buffer(std::vector< unsigned char > &buffer)
Write the state of the module to an array of bytes (wrapped as a memory_stream object)
Definition: colvarmodule.cpp:1928
long long step_number
Use a 64-bit integer to store the step number.
Definition: colvarmodule.h:147
int parse_global_params(std::string const &conf)
Parse the few module's global parameters.
Definition: colvarmodule.cpp:381
static real debug_gradients_step_size
Finite difference step size (if there is no dynamics, or if gradients need to be tested independently...
Definition: colvarmodule.h:332
int run_tcl_script(std::string const &filename)
Run provided Tcl script.
Definition: colvarmodule.cpp:472
int close_traj_file()
Close it (note: currently unused)
std::vector< size_t > depth_v
Thread-specific depth.
Definition: colvarmodule.h:903
static size_t const en_width
Number of characters to represent the collective variables energy.
Definition: colvarmodule.h:761
static std::string to_str(std::vector< real > const &x, size_t width=0, size_t prec=0)
Convert to string for output purposes.
Base class containing parsing functions; all objects which need to parse input inherit from this.
Definition: colvarparse.h:27
Definition: colvarproxy.h:559
Value of a collective variable: this is a metatype which can be set at runtime. By default it is set ...
Definition: colvarvalue.h:43
colvarmodule cvm
Shorthand for the frequently used type prefix.
Definition: colvarmodule.h:960