Modules

ModuleSource FileDescription
aabb_maabb_m.fpp
aabbtree_maabbtree_m.f90

Implements an axis-aligned bounding box (AABB) tree. This code is adapted from the C++ implementation by Lester Hedges. The original C++ implementation can be found here.

   aabbtree_smaabbtree_sm.fpp
atmcfg_matmcfg_m.f90
bd_solver_mbd_solver_m.f90

Routines implementing Brownian Dynamics (BD) solver.

brown_mbrown_m.f90

Contains routines for evaluating B.dW in the SDE for Brownian Dynamics simulation.

cell_list_mcell_list_m.f90

Sorts atoms using a cell list.

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config_io_mconfig_io_m.f90

Routines for IO of config and dump files.

connectivity_mconnectivity_m.f90

Routines for building atom->bond, atom->angle, etc. tables and excluded atoms table.

constants_mconstants_m.f90

Various math constants.

control_mcontrol_m.f90

Routines for reading and witing control file.

ia_angle_mia_angle_m.f90

Angle potentials

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ia_bond_mia_bond_m.f90

This module contains routines to evaluate bond potentials and their derivative.

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ia_dihedral_mia_dihedral_m.f90

Dihedral potentials (none implemented)

ia_external_mia_external_m.f90

External potentials

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ia_tether_mia_tether_m.f90

Tether potentials

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ia_vdw_mia_vdw_m.f90

Routines to evaulate pairwise potentials and their derivative.

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interaction_minteraction_m.f90

Driver routines for force & energy calculation.

logger_mlogger_m.f90

Implements a basic logger.

pairtab_mpairtab_m.fpp
qsort_mqsort_m.f90

Implements quicksort for a sequence of integers and reals, in combination with insertion sort for very short sequences.

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random_mrandom_m.f90

Provides random number generation procedures, mostly calling routine from Intel MKL VSL.

setup_msetup_m.f90

Routines for doing allocation, etc. in preparation for simulation run.

simbox_msimbox_m.f90

Implements a simulation box with appropriate boundary conditions.

stats_mstats_m.f90

Computes and writes properties calculated during simulation.

strings_mstrings_m.f90

Routines for string handling

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table_mtable_m.f90

Implements a table with contiguously stored rows.

timestamp_mtimestamp_m.f90
trajectory_mtrajectory_m.f90

Routines for reading and writing frames from a trajectory file.

utils_math_mutils_math_m.f90

Various (mostly linear algebra) functions, particularly for use with small matrices.

vector_mvector_m.f90

Implements a vector as an extendable array.

module~~graph~~ModuleGraph module~aabbtree_sm aabbtree_sm module~aabbtree_m aabbtree_m module~aabbtree_sm->module~aabbtree_m module~qsort_m qsort_m module~constants_m constants_m module~qsort_m->module~constants_m module~pairtab_m pairtab_m module~pairtab_m->module~constants_m module~pairtab_m->module~aabbtree_m module~atmcfg_m atmcfg_m module~pairtab_m->module~atmcfg_m module~table_m table_m module~pairtab_m->module~table_m module~connectivity_m connectivity_m module~pairtab_m->module~connectivity_m module~vector_m vector_m module~pairtab_m->module~vector_m module~simbox_m simbox_m module~pairtab_m->module~simbox_m module~cell_list_m cell_list_m module~pairtab_m->module~cell_list_m module~strings_m strings_m module~strings_m->module~constants_m module~timestamp_m timestamp_m iso_fortran_env iso_fortran_env module~constants_m->iso_fortran_env module~aabbtree_m->module~strings_m module~aabbtree_m->module~constants_m module~aabbtree_m->module~vector_m module~aabb_m aabb_m module~aabbtree_m->module~aabb_m module~setup_m setup_m module~setup_m->module~strings_m module~setup_m->module~constants_m module~logger_m logger_m module~setup_m->module~logger_m module~random_m random_m module~setup_m->module~random_m module~setup_m->module~atmcfg_m module~bd_solver_m bd_solver_m module~setup_m->module~bd_solver_m module~config_io_m config_io_m module~setup_m->module~config_io_m module~stats_m stats_m module~setup_m->module~stats_m module~trajectory_m trajectory_m module~setup_m->module~trajectory_m module~control_m control_m module~setup_m->module~control_m module~interaction_m interaction_m module~setup_m->module~interaction_m module~setup_m->module~simbox_m module~logger_m->module~timestamp_m module~logger_m->iso_fortran_env module~random_m->module~constants_m mkl_vsl_type mkl_vsl_type module~random_m->mkl_vsl_type mkl_vsl mkl_vsl module~random_m->mkl_vsl module~utils_math_m utils_math_m module~utils_math_m->module~constants_m ieee_arithmetic ieee_arithmetic module~utils_math_m->ieee_arithmetic module~atmcfg_m->module~constants_m module~brown_m brown_m module~brown_m->module~strings_m module~brown_m->module~constants_m module~brown_m->module~logger_m module~brown_m->module~random_m iso_c_binding iso_c_binding module~brown_m->iso_c_binding mkl_lapack mkl_lapack module~brown_m->mkl_lapack mkl_blas mkl_blas module~brown_m->mkl_blas module~bd_solver_m->module~constants_m module~bd_solver_m->module~logger_m module~bd_solver_m->module~atmcfg_m module~bd_solver_m->module~brown_m module~bd_solver_m->module~config_io_m module~bd_solver_m->module~stats_m module~bd_solver_m->module~trajectory_m module~bd_solver_m->module~control_m module~bd_solver_m->module~interaction_m module~bd_solver_m->iso_c_binding module~bd_solver_m->mkl_blas module~config_io_m->module~strings_m module~config_io_m->module~constants_m module~config_io_m->module~atmcfg_m module~config_io_m->module~simbox_m module~table_m->module~constants_m module~table_m->module~vector_m module~stats_m->module~strings_m module~stats_m->module~constants_m module~stats_m->module~atmcfg_m module~stats_m->module~control_m module~stats_m->module~simbox_m module~trajectory_m->module~constants_m module~control_m->module~strings_m module~control_m->module~constants_m module~interaction_m->module~pairtab_m module~interaction_m->module~constants_m module~interaction_m->module~atmcfg_m module~interaction_m->module~table_m module~interaction_m->module~stats_m module~interaction_m->module~control_m module~ia_dihedral_m ia_dihedral_m module~interaction_m->module~ia_dihedral_m module~ia_bond_m ia_bond_m module~interaction_m->module~ia_bond_m module~ia_external_m ia_external_m module~interaction_m->module~ia_external_m module~ia_tether_m ia_tether_m module~interaction_m->module~ia_tether_m module~interaction_m->module~simbox_m module~ia_angle_m ia_angle_m module~interaction_m->module~ia_angle_m module~ia_vdw_m ia_vdw_m module~interaction_m->module~ia_vdw_m module~ia_dihedral_m->module~constants_m module~ia_dihedral_m->module~atmcfg_m module~connectivity_m->module~constants_m module~connectivity_m->module~table_m module~connectivity_m->module~vector_m module~ia_bond_m->module~strings_m module~ia_bond_m->module~constants_m module~ia_bond_m->module~logger_m module~ia_external_m->module~constants_m module~ia_external_m->module~atmcfg_m module~ia_tether_m->module~constants_m module~ia_tether_m->module~atmcfg_m module~vector_m->module~qsort_m module~vector_m->module~constants_m module~simbox_m->module~constants_m module~simbox_m->module~random_m module~aabb_m->module~strings_m module~aabb_m->module~constants_m module~cell_list_m->module~constants_m module~cell_list_m->module~vector_m module~cell_list_m->module~simbox_m module~ia_angle_m->module~constants_m module~ia_angle_m->module~atmcfg_m module~ia_vdw_m->module~constants_m module~ia_vdw_m->module~atmcfg_m program~main main program~main->module~strings_m program~main->module~constants_m program~main->module~setup_m program~main->module~logger_m program~main->module~control_m
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