[-](idf | bdf | wfn) filename
This keyword enters the pathname to a valid Interface Data File (IDF) on disk.
The IDF provides a link between PAMoC and other computer packages, which are able to provide sufficient experimental or theoretical data for calculating/analyzing the electronic density of an isolated molecule or molecular crystal.
PAMoC is interfaced to two main classes of software codes, namely ab initio electronic structure packages and computer programs for multipole refinement of experimental and theoretical structure factors. Eventually, PAMoC accepts other types of IDF (like CIF's and CRYSTAL print-output files), but in these cases the actions that PAMoC can take, are limited by the type and content of the IDF itself, and additional data input may be required.
A list of the IDF's recognized by PAMoC is reported below. Each item in the list is a link to the corresponding page of the manual that provides further details.
VALRAY bdf is the only binary data files recognized by PAMoC. The remaining IDF's are all ascii files. PAMoC distinguishes one from the other because of a specific character string in the first line of each file. In the absence of such a string, the IDF is assumed to be an AIM wavefunction file.
Many popular ab initio quantum chemistry programs can create a traditional AIM wavefunction file (extension .wfn) and, eventually, an extended AIM wave function file (extension .wfx). The extended AIM wavefunction file is a new wavefunction file format originally defined for AIMAll. The .wfx file format is not yet supported by PAMoC.
Here we mention a few general purpose ab initio electronic structure packages which are capable of producing .wfn files that have been submitted to PAMoC successfully:
Among the three ab initio packages mentioned above, only GAMESS is distributed under a "site license at no cost". However there are other ab initio packages that are capable of producing .wfn files and are distributed at no cost, like ORCA (available under a research group license to academic users) and NWCHEM (distributed as open-source under the terms of the Educational Community License version 2.0, ECL 2.0). ORCA has a built-in procedure, instead NWCHEM needs a third-party patch.
VALRAY is a program package for multipole refinement and analysis of electron densities from X-ray diffraction data based on Stewart multipole formalism. It stores and retrieves much of its data on a binary data file (bdf), that PAMoC is able to read.
Alternatively, PAMoC can read a VALRAY ascii data input file, that has to be prepared
by the user, following the instructions in the
VALRAY Users's Manual[1
Stewart, R. F.; Spackman, M. A.; Flensburg, C.
VALRAY User's Manual (Version 2.1), Carnegie-Mellon University, Pittsburg,
and University of Copenhagen, Copenhagen, 2000.].
However, it is mandatory that the first line of the VALRAY input file is REMARK VALRAY,
in order to let PAMoC know which type of IDF it is going to read.
XD is a computer program package
for multipole refinement and analysis of electron densities from X-ray diffraction data based
on Hansen-Coppens multipole formalism.[2
Koritsanszky, T.; Mallison, P.; Macchi, P.; Volkov, A.; Gatti, C.; Richter, T.;
Farrugia, L.:
XD2006. A Computer Program Package for Multipole Refinement, Topological
Analysis of Charge Densities and Evaluation of Intermolecular Enerigies from
Experimental or Theoretical Structure Factors (2007).]
The XD interface data file must contain the identifier XD as the first two characters, in order to let PAMoC recognize the type of interface. Then the names of the Master, Parameter and Databank files follow in this order, unless they are introduced by a keyword. The recognized keyword are:
File-names must not contain any keyword-name as a substring. Any line in the interface data file which begins with either '!' or '#' is a comment line and therefore it is ignored by PAMoC.
An example of XD-interface-data-file (xd.idf) follows:
XD
!the sequence order of the next three lines is mandatory
/home/username/src/pamoc/tests/lala/interfaces/xd.mas
/home/username/src/pamoc/tests/lala/interfaces/xd.res
/home/username/src/pamoc/tests/lala/interfaces/xd.bnk_RHF_CR
|
The same IDF of the previous example can be written in the following way:
XD
!since keywords are being used, the sequence order of the next
!three lines is irrelevant
xdres /home/username/src/pamoc/tests/lala/interfaces/xd.res
xdbnk /home/username/src/pamoc/tests/lala/interfaces/xd.bnk_RHF_CR
xdmas /home/username/src/pamoc/tests/lala/interfaces/xd.mas
|
The interface generates a disk file 'valray.dat' which contains atomic scattering factors (FCORE, FVAL, FLSHEL, FDIPOL, FQUAD, FOCTAP, FHEXAD) and atomic populations (POPVAL) in VALRAY format, available for merging into an input data deck for VALRAY code.
The interface between XD and PAMoC is still in preparation. It has been tested for calculation of outer moments (Stewart pseudoatom) and of intermolecular interactions and lattice energies (Spackman model). Any application which implies a direct evaluation of the electron density is likely to fail.
At the Sagamore XIII conference held at Stare Jablonski, Poland, in 2000, the IUCr Commission
on Charge, Spin and Momentum Densities decided to prepare a CIF dictionary
("rhoCIF")[3
Mallison, P. R.; Brown, I. D.
Classification and use of electron density data
in International Tables for Crystallography, Volume G, Definition and exchange of
crystallographic data.
Hall, S.; McMahon, B. (Eds.); Section 3.5, pp. 141-143. Dordrecht: Springer, 2005,
ISBN: 978-0-470-68910-3.
IUCr online edition, 2006, ISBN: 978-1-4020-3138-0, DOI: 10.1107/97809553602060000107.
] for reporting electron densities in crystals.
The XD program package (starting from its 2003 version) can read and write CIF's which include data items described in the "rhoCIF" dictionary, as well as items in the "coreCIF" dictionary.
PAMoC actually uses a limited implementation of the "rhoCIF" and "coreCIF" dictionaries,
based on the CIFtbx library of Fortran functions for programming CIF
applications.[4
Hall, S. R.; Bernstein, H. J.
J. Appl. Cryst. 1996, 29, 598-603.]
The CIF-IDF must contain the identifier CIF as the first three characters. Then, the name of a standard CIF file follows, not necessarily on the same line. Optionally, an XD-type data-bank file-name (introduced by keywords XDBNK or DBNK) and a set of semicolon-separated dictionary file-names (introduced by keyword DICT) can be provided on separate lines. CIF dictionaries can be defined also through the environment variable CIF_DIC (set externally to PAMoC). Dictionaries defined in the IDF file override those defined externally.
If an XD-type data-bank file (atom wave-function) has been made available, the interface generates a disk file, 'valray.dat', which contains atomic scattering factors (FCORE, FVAL, FLSHEL, FDIPOL, FQUAD, FOCTAP, FHEXAD) and atomic populations (POPVAL) in VALRAY format, available for merging into an input data deck for VALRAY code.
Any line in the interface data file which begins with either '!' or '#' is a comment line and therefore it is ignored by PAMoC.
An example of CIF-interface-data-file (cif.idf) follows:
CIF /pathname/lala.cif
dict /pathname/cif_core.dic:/pathname/cif_rho.dic
xdbnk /pathname/xd.bnk_RHF_CR
!uncomment next line to select a data-set among two or more data-sets in the CIF file
!data data-set-name
|
The CRYSTAL package provides a nuclear-centered multipole expansion of the periodic wave function, based on Mulliken partitioning scheme. Mulliken moments can be used to estimate molecule-molecule electrostatic interaction energies as well as the electrostatic contribution to the crystal lattice energy. The interface-data-file to PAMoC is the union of the output files produced by the CRYSTAL programs crystal (which calculates a periodic wave-function) and properties (which calculates spherical harmonics multipole moments, using the keyword POLI).
The following shell-script illustrates the procedure:
#!/bin/csh # set EXEDIR = $HOME/bin/CRYSTAL98 date >& glycine-crystal98.ext hostname >>& glycine-crystal98.ext $EXEDIR/scfdir < glycine-crystal98.inp >>& glycine-crystal98.ext $EXEDIR/properties << ENDINPUT >>& glycine-crystal98.ext POLI 4 0 -4 END ENDINPUT date >>& glycine-crystal98.ext |
Only a limited number of tests has been made, using versions 1998, 2003 and 2006 of the CRYSTAL package. PAMoC users are kindly invited to report bugs and problems to the author.
CRYSTAL print output files are also recognized by PAMoC as an external-dma file (see keyword ext).
The first line of the promolecule IDF must specify the identifier PROM as the first four characters. The remaining characters on the line may define a title for the job. For a promolecule calculation only the coord block data is needed, unless fractional coordinates are given, in which case also the crystal block data (cell, latt, sym, space) are required. For a procrystal calculation both the coord and the crystal (cell, latt, sym, space) block data are needed. Any line in the IDF beginning with either ! or # is a comment line. Data are provided in the form of a keyword followed by arguments, as shown in the following Table:
| cell | a b c alpha beta gamma | Cell parameters, with lengths in angstrom or 1/angstrom and angles in degrees or cosines of angles. |
| latt | x y | x is either A or C, for Acentric or Centrosymmetric crystal respectively, and y specifies the lattice type as P,I,R,F,A,B,C. |
| sym|symm|symtry | symmetry operation elements | The symmetry operation elements are given exactly as in the International Tables, the three general position coordinates being separated either by commas or spaces. More than one position may be given within one sym entry, if desired, by placing a semicolon between each of them. Alternatively, the symmetry operation is written in a purely numerical way by giving a translation vector and a 3 by 3 rotation matrix, i.e.: tx r11 r12 r13 ty r21 r22 r23 tz r31 r32 r33. |
| spac[e group] | number | symbol | A space group can be specified either by its International Tables number (1 through 230) or by its symbol. Explicit definition of the space group is an alternative to specify the lattice type (latt) and symmetry operations (sym) separately. |
| coord | [units] [number-of-atoms] | The units of atomic coordinates can be specified as fract[ional] (the default), angstrom, bohr, au. Atom coordinates must follow this line, on separate lines, one for each atom. If the number-of-atoms is omitted, coordinate lines will be read until either the end-of-file or an end line is encountered. Any coordinate line must have either 4 fields, i.e. Symb X Y Z or 5 fields, i.e. IAn Symb X Y Z |
An example of promolecule-interface-data-file (h2o.idf) follows:
PROM h2o
COORD BOHR
O 0.00000000 2.29990442 1.53036069
H 0.00000000 3.74285016 2.60003072
H 0.00000000 0.85696057 2.60003072
END
|