Control and Prediction of the Organic Solid State

System Requirements and Compiler issues

Please check our recommendations for the computer system and compilers.

Known limitations of programs

NEIGHCRYS copes with only some Z'<1 input files. The utility Autosymm is being distributed with the current bundle, which can be used to increase the symmetry to Z'=1 in most cases.
Automated symmetry reduction is not currently possible with anisotropic repulsion potentials, because of the need to generate the atoms typing and local axes for the new independent molecule in the asymmetric unit cell.
Only one Tang-Toennies damping parameter can be specified for the entire molecule, whereas more recent research (A J Misquitta, 2013, J Chem Theory Comput, 9, 5313) suggests that induction damping parameters may be more accurately defined by atomic type.
Linear molecules cannot be dealt with by NEIGHCRYS.
In the case of symmetry reduction, the output energy is calculated per formula unit of the original cell, so as to keep it directly comparable with non-symmetry-reduced structures. Z in the output fort.16 file is crystallographically incorrect, but will allow repeated calculations to keep directly comparable energies.

Current release versions

DMACRYS version 2.3.0 and NEIGHCRYS version 2.3.0

These versions of the codes contain the following improvements on previous versions.

All 2.x.x versions of the codes are not compatible with 1.x.x versions.
Addition of splines to smooth off potential at cutoff distances, and hence give better numerical derivatives with moderate cutoffs
Inclusion of induction energy using distributed dipolar polarisability models
Include (damped) C6 C8 and C10 isotropic dispersion
In the development version of the program, 2.2.1.0, the splines were incorrectly summed over the charge-dipole and dipole-dipole terms. This has been fixed, but may lead to small discrepancies in output.
NEIGHCRYS 2.1.0 and DMACRYS 2.1.0 have been changed to reduce time spent in repeated setting up of intramolecular connectivity data for very large molecules. (This was implemented incorrectly in 2.1.0, with the scaling from lattice units to Angstroms not carried out, but is fixed in 2.2.0.)
DMACRYS 2.2.0 (and higher) writes out the symmetric component of the hessian, and can read this in at the start of subsequent runs to reduce time. This is used with the keyword HESS in the *.dmain.

Reported bugs

NEIGHCRYS now carries out checks for crystallographic consistency of input structures. This does not support unusual settings of some spacegroups. Some DMACRYS symmetry reduction runs produce structures in unusual spacegroup settings, so further runs are not possible without manual intervention to rest the spacegroup.
Versions of NEIGHCRYS higher than 2.0.8 do not seem to be reading in .fdat files output from MOLPAK. If you are using MOLPAK, contact us for the 2.0.8 version of NEIGHCRYS and DMACRYS.

Ongoing developments

NEIGHCRYS can now generate a molecular axis definition file and an anisotropic axis system file automatically. These are currently only working for Z'=1 single component systems. This is being tested further and made more comprehensive.
This capability will be extended to automatic generation of anisotropic axes for symmetry reduction cases.

Please email DMACRYS Support if there is anything you want to add to this page. If you spot a new problem, let her know, or if you have anything further to add to an existing problem. Also, if you have solved the problem, email DMACRYS Support to remove it from the list.

Previous versions

Known problems with DMAREL

d packing types from MOLPAK have density out by a factor of 2.

Known problems with previous release version (2.0.8) of DMACRYS

Although the code should not allow zero to appear as a negative number, this still seems to be occuring with some compilers. This leads to differences in the NEIGHCRYS generated *.dmain, and subsequent differences in the *.dmaout files and fort.12 output in the case of properties calculations. This causes the test suite to appear to fail on tests 11, 12 and/or 13. Detailed analysis of the fort.12 (run diff on the file provided and the user-generated output) will only show changes in the signs of some zeros.
The DMACRYS output fort.16 has a ZERR line reporting that the numbers are only accurate to 1 decimal place ("0.0" accuracy in each parameter), which was intended to flag up that this is a computer-generated structure. If this input is used in some crystallographic programs that use ZERR, for example the Mercury conversion of the .res file to .cif format, it leads to inaccurate cell parameters rounded to this accuracy. This can be avoided by removing all the 0.0 error estimates. In the next release, this will be the default output.
When NEIGHCRYS is used to reduce symmetry, the output dmacrys.new.axis has the inverted molecules included. This causes some problems with running NEIGHCRYS on the subsequently reduced symmetry structure. These inverted molecule definitions will be removed from this file in the next version of NEIGHCRYS.
When DMACRYS is run without symmetry (SYMM is removed and information in fort.20 is not used), the resulting fort.16 is missing information on atom types (in the SYMM and atom lines).
When DMACRYS is minimizing a cell which is a long needle or a thin plate, the program assumes that you will always need to sum more than 1 reciprocal lattice vector in each direction, but for plates or needles it sometimes works out a value of 1. If you encounter this problem, please email Louise and registered users will be sent a new version of the program.
In the development version of the program, 2.2.1.0, the splines are incorrectly summed over the charge-dipole and dipole-dipole terms. This can lead to incorrect imaginary phonon frequencies.

Known problems with previous release version (1.11) of DMACRYS

There are some problems with symmetry reduction.
DMACRYS does not work for spherical ions (eg Cl^-).

Known problems with previous release version (1.10) of NEIGHCRYS

It standardises all OH bond lengths to 0.976 Å (neutron value from Allen, F. H.; Kennard, O.; Watson, D. G.; Brammer, L.; Orpen, A. G.; Taylor, R. Tables of bond lengths determined by x-ray and neutron diffraction. Part 1. Bond lengths in Organic compounds. Journal of the Chemical Society-Perkin Transactions 2 1987, (12), S1-S19.), which is not appropriate for carboxylic acids or water.
An extra line, reporting the number of times the primitive cell appears in the unit cell, was introduced, for use with DMAflex2
NEIGHCRYS assigns S as silicon for .fdat files, although .res files it is correctly assigned as sulfur.

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