Procedures

Calculates the center of an aabb.

Calculates the surface area of an aabb.

Clears all attributes of an AABB and sets them to zero.

Fattens an AABB by a fraction of its base extent.

Calculates the extent of an aabb. The extent of an AABB is defined as the difference between its upper and lower bounds.

Returns true if this includes other, false otherwise. Inclusion is considered in a strict sense.

Initializes an aabb_t instance from lower and upper bounds.

Returns true if this overlaps other, false otherwise. Touching does not count as an overlap.

Prints an AABB.

Combines AABBs x and y to return a new AABB z.

Updates an AABB with new bounds.

Adds a square matrix and its transpose in place: $A_{ij} = A_{ij } + A_{ji}$

Checks if two arrays are elementwise close within tolerance

Checks if two rank-1 floating point arrays of type double are close within tolerance.

Checks if two rank-2 floating point arrays of type double are close within tolerance.

Checks if two rank-3 floating point arrays of type double are close within tolerance.

Setter for angular cosine interaction.

Deallocates all memory acquired by a configuration_t object and resets all other components to zero. Exception: num_coeffs is not reset to zero.

Clears up memory allocated in bds_init.

Initializes the BD solver.

Driver for BD integrator.

Calculates energy & its derivative for FENE bond. See bond_fene_set.

Setter for FENE bond.

Calculates energy & its derivative for harmonic bond. See bond_harm_set.

Setter for harmonic bond interaction.

Calculates energy & its derivative for Kremer-Grest bond. See bond_kg_set.

Setter for FENE bond interaction.

Evaluates the potential & its derivative for Marko-Siggia bond. See bond_ms_set.

Setter for Marko-Siggia bond.

Main driver routine for calculating B.dW.

Calculates standard normally distributed random vectors.

Performs cleanup.

Performs initial setup.

Builds a pair table using cell list.

Builds a pair table using direct N^2 looping over all pairs.

Builds a pair table using the Verlet scheme.

Implements block Lanczos algorithm for calculating B.dW.

Calculates B.dW using Cholesky decomposition.

Implements Lanczos algorithm for calculating B.dW.

Calculates the diffusion term of the SDE. Updates module variables diffusion and cntr_mobsam.

Calculates the drift term of the SDE.

Calculates the RPY approximation to the mobility tensor.

Sorts atoms into cells for calculating short-range interations

Makes a table of neighboring cells.

Deallocates memory allocated in cl_init.

Returns a pointer to the entries of cell with linear index ic.

Returns a pointer to the neighbor cells of cell with linear index ic.

Returns the total number of cells

Initializes a cell list.

Prints a cell list

Sets the cell size. The actual cell size may be slightly larger.

Computes statistics for a single chain in unbounded domain.

Computes statistics for possibly multiple chains in a periodic domain.

Reads simulation control parameters from file

Write simulation parameters to file

Calculates the cross product between two 3-element vectors

Calculates the cross product matrix of a 3-element vector. The cross product matrix A of a is defined as a x b = A . b, where b is another 3-element vector.

Deletes a BRNG stream.

Returns the determinant of an (N x N) matrix, where N = 2, 3, or 4.

Sorts a sequence of reals

Calculates the eigenvalues of a symmetric 3x3 matrix A using Cardano's analytical algorithm. Only the diagonal and upper triangular parts of A are accessed. The access is read-only.

Adds an element to the end of a dvector. Reallocation will take place if required.

Copies the contents of dvector other to dvector this

Clears a dvector. Access allowed after a call to clear.

Deletes a dvector. No access is allowed to this object after this call.

Creates a dvector with all elements from an array

Returns a pointer to the underlying data of a dvector

Returns the length of a dvector

Returns the ith element of a dvector.

Creates an empty dvector with all elements equal to zero.

Removes the last element and returns it. Calling this method on an empty list

Prints a dvector

Resizes a vector to a given size. Existing data is truncated if desired size is smaller than current size. Otherwise, the empty spaces are filled with zero.

Sets the value of the ith element of a dvector. No bounds check is performed.

Releases additional memory to fit underlying data of a dvector to a size this%len_init.

Sorts a dvector in ascending order. If order is provided, it will contain the sorted indices. The size of order must be at least this%len.

Sorts and removes all duplicate entries of a dvector. Note that the internal buffer size remains unchanged. To reduce the buffer size, call dvector_shrink_to_fit.

Calculates the eigenvalues of a 3 x 3 real symmetric matrix. The eigenvalues calculated are in decreasing order. Only the diagonal and lower triangular part of the matrix is accessed.

Before a call to this first build atbo_tab.

Returns the diagonal elements of a square matrix.

Returns a random integer from a uniform distribution.

Calculates the quadratic form x^T A x, where A is an n x n matrix and x is a vector of length n

Generates a random vector of integers from a gaussian distribution.

Returns a random vector of integers from a uniform distribution.

Returns a random vector from a uniform distribution.

Returns a random number from a uniform distribution.

HMS_CURRENT_HMS returns the current HMS time as integers.

HMS_CURRENT_PRINT prints the current HMS time, and a user specified string.

HMS_CURRENT_STRING writes the current HMS data into a string.

HMS_DELTA_PRINT prints the change in HMS time, and a user specified string.

Copies the contents of ivector other to dvector this. Integers are cast to reals.

Calculates forces & energy due to all angles. Will add to energy_angle & 'forces`.

Calculates forces & energy due to all bonds. Will add to energy_bond & and 'forcesin modulem_globals`.

Calculates forces & energy due to all dihedrals. Will add to energy_dihedral & 'forces`.

Calculates the force and energy due to an external field and adds to energy_external, 'forces, &stress`.

Calculates forces & energy due to all tethers. Will add to energy_tether & 'forces`. Tether forces are not subject to periodic boundary conditions.

Calculates force and energy due to all short-ranged non-bonded pairwise interactions based on pair_tab.

Sets up parameters for angle potentials

Sets up parameters for bond potentials

Calculates total forces and energies

Sets up parameters for dihedral potentials

Sets up parameters for external potentials. Usually there is nothing to set for externals, but this acts as a placeholder for special cases.

Cleanup routine for interaction calculation.

Calculates the energy & force due to an angle.

Calculates the energy & its derivative due to a bond.

Calculates the force & energy due to a dihedral.

Calculates the energy and its derivative due to a tether.

Calculates the energy & its derivative due to a single interacting pair of atoms.

Builds necessary neighbor tables and sets up parameters for potentials.

Sets up parameters for tether potentials

Sets up parameters for vdw potentials

Creates an identity matrix of size n x n.

Initializes a BRNG stream.

Performs one step of BD integration using explicit Euler-Maruyama scheme.

Performs one step of BD integration using semi-implicit Euler scheme.

Inverts a 3x3 matrix.

Sorts a sequence of integers

Checks if two floating point numbers of type double are close within tolerance.

Appends an element val to row irow.

Clears all rows. Does not deallocate memory.

Deletes an itable_t. No access is allowed to this object after this call.

Returns a pointer to the row data of irow. No bounds checking is performed.

Returns the jth element of row irow

Creates an empty itable_t with num_rows rows and all rows having zero elements.

Returns .true. if val is in row irow, .false. otherwise.

Prints an itable_t.

Sets the value of the jth element of row irow.

Releases additional memory to fit underlying data.

Adds an element to the end of an ivector. Reallocation will take place if required.

Copies the contents of ivector other to ivector this

Clears an ivector. Access allowed after a call to clear.

Deletes an ivector. No access is allowed to this object after this call.

Creates an ivector with all elements from an array

Returns a pointer to the underlying data of an ivector

Returns the length of an ivector

Returns the ith element of an ivector.

Creates an empty ivector with all elements equal to zero.

Removes the last element and returns it. Calling this method on an empty list

Prints an ivector

Resizes a vector to a given size. Existing data is truncated if desired size is smaller than current size. Otherwise, the empty spaces are filled with zero.

Sets the value of the ith element of an ivector. No bounds check is performed.

Releases additional memory to fit underlying data of an ivector to a size this%len_init.

Sorts an ivector in ascending order. If order is provided, it will contain the sorted indices. The size of order must be at least this%len.

Sorts and removes all duplicate entries of an ivector. Note that the internal buffer size remains unchanged. To reduce the buffer size, call ivector_shrink_to_fit.

Generates evenly spaced numbers over a specified interval. Both end points are included. If start < finish, the returned step size (if step is present) will be negative.

Loads a BRNG stream from file fn.

Cleanup routine for a logger_t instance.

Initializes a logger.

Write a message to the log file.

Generates numbers spaced evenly on a log scale. In linear space, the sequence starts at base ** start (base to the power of start) and ends with base ** stop

Multiplies a matrix with its transpose: $\mathbf{\mathrm{B}} = \mathbf{\mathrm{A}} \cdot \mathbf{\mathrm{A}}^T$

Orthogonalizes a set of vectors in-place using Gram-Schmidt orthonormalization

Calculates the outer product of two vectors, $c_{ij} = a_i b_j$.

Builds a pair table. The resulting table is stored in the module variable pair_tab.

Cleanup for pair list calculation.

Performs initial setup for building a pair list.

Generates a random vector from the surface of a unit sphere.

Read from CONFIG file

Reads from DUMP file

Reads a line from unit=nunitr, ignoring blank lines and deleting comments

Saves the RNG seed to file fn.

Saves a BRNG stream to file fn.

Returns the scalar triple product a.(b x c)

Calculates the nonlinear function.

Calculates jacobian times vector product. This is a dummy subroutine.

Specifies this as non-deforming.

Returns the image of r under PBC.

Returns uniformly distributed points within the box.

Initializes an instance of smbx_t. Can also be called to reset.

Sets all three basis vectors.

Adjusts atom positions such that the c.o.m. of the atoms is at the center of the box. Assumes all atoms to have the same mass and aligned axis. Optionally returns the original c.o.m.

Adjusts atom positions such that the c.o.m. of the atoms is at the origin. Assumes all atoms to have the same mass and aligned axis. Optionally returns the original c.o.m.

Specifies this as deforming.

Wraps atom positions w.r.t. periodic boundary conditions.

Accumulates statistics.

Clean up for stats collection.

Set up for stats collection

Writes statistics to fn_stats.

Appends a copy of the source string to the dest string, with optional string sep in between. It is assumed that dest is long enough to hold the result, otherwise an error will be generated.

Returns a copy of str with multiple spaces and tabs converted to single spaces, control characters deleted, and leading and trailing spaces removed.

Compact a string representing a real number, so that the same value is displayed with fewer characters.

Deletes first n occurrences of substring substr from string str and shifts characters left to fill hole. If n < 0, all occurances are deleted. If n is not explicitly provided, it defaults to removing the first occurrence. Trailing spaces or blanks are not considered part of substr.

Returns .true. if the string str ends with suffix, otherwise return .false.. With optional start, test beginning at that position. With optional finish, stop comparing beyond that position.

Generic interface for writing a number to a string. The calling syntax is str_from_num(num, frmt) where number is a real number or an integer, format is the format desired, e.g., e15.6, i5, etc.

Split a string str into two strings, key and val based on space delimiter.

Inserts the string substr into the string str at position loc. Characters in str starting at position loc are shifted right to make room for the inserted string. Trailing spaces of substr are removed prior to insertion.

Returns .true. if line is a comment, .false. other wise.

Returns .true. if str contains only digits (0,1,...,9) and .false. otherwise.

Returns .true. if str contains only letters (a--z or A--Z) and .false. otherwise.

Returns .true. if str is non-empty and contains only whitespace characters (tab or blankspace). Otherwise .false. is returned.

This routine finds the delimiter in string str that matches the delimiter in position ipos of str. The argument imatch contains the position of the matching delimiter. Allowable delimiters are (), [], {}, <>.

Returns a copy of the string str with spaces, tabs, and control characters removed.

Shifts characters in str by n positions (positive values denote a right shift and negative values denote a left shift). Characters that are shifted off the end are lost. Positions opened up by the shift are replaced by spaces.

Routine finds the first instance of a character from delims in the the string str. The characters before the found delimiter are output in before. The characters after the found delimiter are output in str. Repeated applications of this routine can be used to parse a string into its component parts. Multiple whitespaces of str are compacted into a single whitespace before splitting begins. If either str or delimiter is empty, an empty string is retured in before and str remains unchanged.

Returns .true. if the string str starts with prefix, otherwise returns .false.. With optional start, test beginning at that position. With optional finish, stop comparing beyond that position.

Returns a copy of string str with the leading and trailing characters removed. The chars argument is a string specifying the set of characters to be removed. The chars argument is not a prefix or suffix; rather, all combinations of its values are stripped. If ends = 'l', only leading characters are removed, if ends = 'r', only trailing characters are removed, and if ends = 'b' both leading and trailing characters are removed.

Strips trailing comment from a string.

This function returns a string that is like the string str with all characters that are not between a pair of quotes ("..." or '...') converted to lowercase.

This function returns a string that is like the string str with all characters that are not between a pair of quotes ("..." or '...') converted to uppercase.

Deletes nonsignificant trailing zeroes from number string str. If number string ends in a decimal point, one trailing zero is added.

Calculates the difference of a square matrix and its transpose in place: $A_{ij} = A_{ij } - A_{ji}$

Swaps two arrays

Calculates energy and its derivative for harmonic tether interaction. See teth_harm_set.

Setter for harmonic tether interaction.

Not implemented, needs constraint formalism. See teth_rigid_set.

Setter for rigid tether interaction.

TIMESTAMP prints the current YMDHMS date as a time stamp.

TIMESTRING writes the current YMDHMS date into a string.

Returns the trace of a square matrix

Write a frame to an open trajectory

Closes the underlying file of a trajectory_t.

Creates a trajectory_t object with a new underlying file named fn. If fn already exists, it will be truncated. The file fn is opened for both reading and writing.

After a call to this subroutine, all memory within this is deallocated, all components of this are reset to zero, and the underlying file is closed (if open).

Creates a trajectory_t object with a prexisting underlying file named fn. If fn does not exist, an error will be generated. If mode == 'rw', the file fn is opened for both reading and writing. If mode == 'r', the file fn is opened only for reading.

Read from an open trajectory.

Write a frame to an open trajectory

Normalizes a vector in-place. If the magnitude of the vector is nearly zero, no normalization takes place and the vector is returned as is with a warning message.

Evaluates the potential and its derivative for cosine interaction. See vdw_cosine_set.

Setter for cosine interaction.

Evaluates the potential and its derivative for standard DPD interaction. See vdw_dpd_set.

Setter for standard DPD interaction.

Calculates energy & its derivative for gaussian interaction. See vdw_gaussian_set.

Setter for gaussian interaction. The potential is truncated and force-shifted.

Evaluates the potential and its derivative for LJ interaction. See vdw_lj_set.

Evaluates the potential and its derivative for Coulombic interaction combined with 12-6 LJ (cut & shifted). See vdw_lj_coul_set.

Evaluates the potential and its derivative for screened Coulombic interaction combined with 12-6 LJ (cut & shifted). See vdw_lj_coul_debye_set.

Setter for 12-6 LJ with screened Coulombic interaction.

Setter for 12-6 LJ with Coulombic interaction.

Setter for 12-6 LJ (truncated & force-shifted) interaction.

Returns the vector triple product d = a x (b x c)

Write to cfg file

Writes to DUMP file.

Writes header of the file fn_stats.

Write to a LAMMPS data file.

Write to an XYZ file.