Procedures

Calculates energy for angular cosine interaction. params(1) = k

Calculates energy for harmonic angular interaction. params(1) = k

Calculates energy for tabulated interaction.

Setter for tabulated interaction. params(1) = vtltmin, params(2) = vtgtmax, params(3) = intrp_meth, params(4) = flag_bc cache(1) = tmin, cache(2) = tmax

BASIS_FUNCTION_B_VAL evaluates the B spline basis function.

BASIS_FUNCTION_BETA_VAL evaluates the beta spline basis function.

BASIS_MATRIX_B_UNI sets up the uniform B spline basis matrix.

BASIS_MATRIX_BETA_UNI sets up the uniform beta spline basis matrix.

BASIS_MATRIX_BEZIER sets up the cubic Bezier spline basis matrix.

BASIS_MATRIX_HERMITE sets up the Hermite spline basis matrix.

BASIS_MATRIX_OVERHAUSER_NUL sets the nonuniform left Overhauser basis matrix.

BASIS_MATRIX_OVERHAUSER_UNI sets the uniform Overhauser spline basis matrix.

BASIS_MATRIX_OVERHAUSER_UNI_L sets the left uniform Overhauser basis matrix.

BASIS_MATRIX_OVERHAUSER_UNI_R sets the right uniform Overhauser basis matrix.

BASIS_MATRIX_TMP computes Q = T * MBASIS * P

BC_VAL evaluates a parameterized N-th degree Bezier curve in 2D.

BEZ_VAL evaluates an N-th degree Bezier function at a point.

Calculates energy for FENE bond interaction. If bond length exceeds maximum extensible spring length, an error will be reported as ierr = 1. params(1) = kspring, params(2) = r0, params(3) = delta

Calculates energy for harmonic bond interaction.

Calculates energy for Kremer-Grest bond interaction. If bond length exceeds maximum extensible spring length, an error will be reported as ierr = 1.

Setter for FENE bond interaction. params(1) = kspring, params(2) = r0, params(3) = eps, params(4) = sigma cache(1) = r0^2, cache(2) = sigma^2, cache(3) = 2^(1/6)*sigma

Calculates energy for tabulated interaction.

Setter for tabulated interaction. params(1) = vtltmin, params(2) = vtgtmax, params(3) = intrp_meth, params(4) = flag_bc cache(1) = tmin, cache(2) = tmax

BP01 evaluates the Bernstein basis polynomials for [0,1] at a point.

BPAB evaluates the Bernstein basis polynomials for [A,B] at a point.

BPAB_APPROX evaluates the Bernstein polynomial approximant to F(X) on [A,B].

CHFEV evaluates a cubic polynomial given in Hermite form.

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

Clears out all configuration related variables in module m_globals.

DATA_TO_DIF sets up a divided difference table from raw data.

DIF_VAL evaluates a divided difference polynomial at a point.

Sorts a sequence of reals

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.

Prints a dvector

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.

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.

Sets up parameters for angle potentials

Sets up parameters for bond potentials

Calculates total angular energy. Will overwrite energy_angle in module m_globals.

Calculates the angle energy due to a single atom.

Calculates the bond energy of a single atom.

Calculates the dihedral energy due to a single atom.

Calculates the tether energy due to a single atom.

Calculates the pair energy of a single atom. No Verlet list is used.

Calculates the pair energy of a single atom using Verlet list. The Verlet list takes care of excluded atoms.

Calculates total bond energy. Will overwrite energy_bond in module m_globals.

Calculates total dihedral energy. Will overwrite energy_dihedral in module m_globals.

Calculates total energy

Calculates total energy due to external fields. Will overwrite energy_external in module m_globals.

Calculates total tether energy. Will overwrite energy_tether in module m_globals.

Calculates total energy due to short-ranged non-bonded pairwise interactions. Uses direct N^2 calculation. Will overwrite energy_vdw in module m_globals.

Calculates total energy due to short-ranged pairwise interactions. Uses Verlet list. The Verlet list takes care of excluded atoms.

Sets up parameters for dihedral potentials

Sets up parameters for external potentials. Placeholder.

Calculates the energy due to an angle potential.

Calculates the energy due to a bond.

Calculates the energy due to a dihedral.

Calculates the energy due to an external field.

Calculates the energy due to a tether.

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

Sets up parameters for potentials

Sets up parameters for tether potentials

Sets up parameters for vdw potential.

Sorts a sequence of integers

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

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.

Prints an ivector

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.

LEAST_SET defines a least squares polynomial for given data.

LEAST_SET_OLD constructs the least squares polynomial approximation to data.

LEAST_VAL evaluates a least squares polynomial defined by LEAST_SET.

LEAST_VAL2 evaluates a least squares polynomial defined by LEAST_SET.

LEAST_VAL_OLD evaluates a least squares polynomial defined by LEAST_SET_OLD.

Performs crankshaft move (including end-bond rotation) on an unbranched chain or ring. End-bond rotation will not be performed for rings.

Performs double pivot move (for rings). Does not use Verlet list.

Performs displacement move.

Performs a pivot move. Does not use a Verlet list.

Performs a restricted pivot move on the backbone. Does not use a Verlet list. Unlike usual pivot, the rotation axis for is chosen along the bond incident to the pivot point. This move may be useful for molecules that are restricted to be in a stretched conformation or if angular constraints need to be respected.

Performs side chain crankshaft move.

Performs pivot move on side chains. Does not use Verlet list.

PARABOLA_VAL2 evaluates a parabolic interpolant through tabular data.

PENTA solves a pentadiagonal system of linear equations.

R83_MXV multiplies an R83 matrix times a vector.

R83_NP_FS factors and solves an R83 system.

R83_UNIFORM randomizes an R83 matrix.

R85_NP_FS factors and solves an R85 linear system.

R85_PRINT prints an R85 matrix.

R85_PRINT_SOME prints some of an R85 matrix.

R8_SWAP swaps two real values.

R8_UNIFORM_01 is a portable pseudorandom number generator.

R8GE_FS factors and solves an R8GE system.

R8VEC_BRACKET searches a sorted R8VEC for successive brackets of a value.

R8VEC_BRACKET3 finds the interval containing or nearest a given value.

R8VEC_DISTINCT is true if the entries in an R8VEC are distinct.

R8VEC_EVEN returns N real values, evenly spaced between ALO and AHI.

R8VEC_INDICATOR sets an R8VEC to the indicator vector.

R8VEC_ORDER_TYPE determines the order type of an R8VEC.

R8VEC_PRINT prints an R8VEC.

R8VEC_SORT_BUBBLE_A ascending sorts an R8VEC using bubble sort.

R8VEC_UNIFORM_01 returns a unit pseudorandom R8VEC.

R8VEC_UNIQUE_COUNT counts the unique elements in an unsorted R8VEC.

Generates a random vector from the surface of a unit sphere. Algorithm from Allen & Tildesley (ed 1) p. 349.

Read from CONFIG file

Read config file corresponding to version mcpak-0.1.

Reads simulation parameters from file

Reads from DUMP file

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

SPLINE_B_VAL evaluates a cubic B spline approximant.

SPLINE_BETA_VAL evaluates a cubic beta spline approximant.

SPLINE_BEZIER_VAL evaluates a cubic Bezier spline.

SPLINE_CONSTANT_VAL evaluates a piecewise constant spline at a point.

SPLINE_CUBIC_SET computes the second derivatives of a piecewise cubic spline.

SPLINE_CUBIC_SET_FULL computes second derivatives of piecewise cubic spline.

SPLINE_CUBIC_VAL evaluates a piecewise cubic spline at a point.

SPLINE_CUBIC_VAL2 evaluates a piecewise cubic spline at a point.

SPLINE_HERMITE_SET sets up a piecewise cubic Hermite interpolant.

SPLINE_HERMITE_VAL evaluates a piecewise cubic Hermite interpolant.

SPLINE_LINEAR_INT evaluates the integral of a piecewise linear spline.

SPLINE_LINEAR_VAL evaluates a piecewise linear spline at a point.

SPLINE_OVERHAUSER_NONUNI_VAL evaluates the nonuniform Overhauser spline.

SPLINE_OVERHAUSER_UNI_VAL evaluates the uniform Overhauser spline.

SPLINE_OVERHAUSER_VAL evaluates an Overhauser spline.

SPLINE_PCHIP_SET sets derivatives for a piecewise cubic Hermite interpolant.

SPLINE_PCHIP_VAL evaluates a piecewise cubic Hermite function.

SPLINE_QUADRATIC_VAL evaluates a piecewise quadratic spline at a point.

Calculates and accumulates production statistics

Set up for stats collection

Writes production statistics and zeros out accumulators

Writes equilibration statistics

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.

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 occurance. 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 is empty 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 energy for fene tether interaction.

Calculates energy for harmonic tether interaction.

TIMESTAMP prints the current YMDHMS date as a time stamp.

TIMESTRING writes the current YMDHMS date into a string.

Brings the center-of-mass of the molecule to the origin.

Write a frame to an open trajectory

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).

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.

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

Calculates energy for Gaussian interaction. params(1) = A, params(2) = B, params(3) = rcut cache(1) = V(rcut)

Setter for Gaussian interaction. params(1) = A, params(2) = B, params(3) = rcut cache(1) = V(rcut)

Calculates energy for hard sphere interaction. Overlap will be indicated with ierr = 1. params(1) = r1, params(2) = r2, params(3) = tol

Calculates energy for LJ interaction. params(1) = eps, params(2) = sigma, params(3) = rcut cache(1) = sigma**2, cache(2) = U(rcut)

Setter for LJ interaction. params(1) = eps, params(2) = sigma, params(3) = rcut cache(1) = sigma**2, cache(2) = U(rcut)

Calculates energy for square well interaction. Overlap will be indicated with ierr = 1. params(1) = eps, params(2) = sigma, params(3) = width

Calculates energy for tabulated interaction.

Setter for tabulated interaction. params(1) = vtltmin, params(2) = vtgtmax, params(3) = intrp_meth, params(4) = flag_bc cache(1) = tmin, cache(2) = tmax

Write to cfg file

Write simulation parameters to file

Writes to DUMP file

Write to a LAMMPS data file.

Write to an XYZ file.