ZMATRIX_IO contains procedures for reading and writing Z-matrix files in DYNAMO format.
The DYNAMO Z-matrix format is defined in chapter 12 of the book A Practical Introduction to the Simulation of Molecular Systems.
Module | Variables |
---|---|
CONSTANTS | UNDEFINED |
DEFINITIONS | DP |
ELEMENTS | MASS |
FILES | NEXT_UNIT |
IO_UNITS | INPUT, OUTPUT |
PARSING | Most public items in the module. |
STATUS | ERROR |
ATOMS | Most public items in the module. |
SEQUENCE | Most public items in the module. |
SYMMETRY | Most public items in the module. |
ZMATRIX | Most public items in the module. |
None.
There are three public subroutines in this module.
Subroutine | Purpose |
---|---|
ZMATRIX_DEFINE | Read a DYNAMO Z-matrix file and redefine the system. |
ZMATRIX_READ | Read a DYNAMO Z-matrix file using an existing system definition. |
ZMATRIX_WRITE | Write a DYNAMO Z-matrix file for the current system. |
Argument | Type | Intent | Optional | Purpose |
---|---|---|---|---|
FILE | Character ( Len = * ) | In | Yes | The Z-matrix file name. |
Error | Meaning |
---|---|
I/O Error. | There is a problem with the Z-matrix file. |
Invalid atoms, residue or subsystem counter. | The number of atoms, residues or subsystems is zero or negative. |
SUBSYSTEM label invalid. | There is no "Subsystem" tag. |
SUBSYSTEM name length invalid. | The subsystem name is either too short or too long. |
Two SUBSYSTEM names are the same. | Two subsystems have the same name. |
Invalid number of residues in a subsystem. | The number of residues in the subsystem is either zero or negative or so large that the number of residues specified at the top of the file is exceeded. |
RESIDUE label invalid. | There is no "Residue" tag. |
RESIDUE number invalid. | The residue number does not correspond to that expected in the sequence. |
RESIDUE name length invalid. | The residue name is either too short or too long. |
Invalid number of atoms in a residue. | The number of atoms in the residue is either zero or negative or so large that the number of atoms specified at the top of the file is exceeded. |
ATOM name length invalid. | The atom name is either too short or too long. |
Two ATOM names are the same. | Two atoms in a residue have the same name. |
ATOM or RESIDUE number mismatch. | The numbers of atoms or residues obtained after reading the file do not correspond to the numbers given at the top of the file. |
Argument | Type | Intent | Optional | Purpose |
---|---|---|---|---|
FILE | Character ( Len = * ) | In | Yes | The Z-matrix file name. |
Error | Meaning |
---|---|
I/O Error. | There is a problem with the Z-matrix file. |
Invalid atoms, residue or subsystem counter. | The number of atoms, residues or subsystems does not correspond to that of the system already defined. |
SUBSYSTEM label invalid. | There is no "Subsystem" tag. |
SUBSYSTEM name length invalid. | The subsystem name is either too short or too long. |
SUBSYSTEM name mismatch. | The subsystem in the file does not correspond to that expected from the sequence. |
Invalid number of residues in a subsystem. | The number of residues in the subsystem does not correspond to that expected from the sequence. |
RESIDUE label invalid. | There is no "Residue" tag. |
RESIDUE number invalid. | The residue number does not correspond to that expected in the sequence. |
RESIDUE name length invalid. | The residue name is either too short or too long. |
RESIDUE name mismatch. | The residue name does not correspond to that expected from the sequence. |
Too many atoms in a residue. | There are too many atoms for a residue. |
ATOM name length invalid. | The atom name is either too short or too long. |
ATOM number mismatch. | There is a mismatch in the atomic numbers of equivalent atoms. |
ATOM name mismatch. | There is an unknown atom in the Z-matrix file or there is an atom missing. |
Argument | Type | Intent | Optional | Purpose |
---|---|---|---|---|
FILE | Character ( Len = * ) | In | Yes | The Z-matrix file name. |
Error | Meaning |
---|---|
The ATOMS and ZMATRIX modules are inconsistent. | There is an inconsistency between the definitions given in the ATOMS and ZMATRIX data structures. |
I/O Error. | There is a problem with the Z-matrix file. |
Stable.