Firefly and PC GAMESS-related discussion club
Learn how to ask questions correctly
the following is the complete list of keywords of $ZMAT group as of Firefly version 7.1.G that are not covered by the INPUT.DOC file at moment:
- IFRZAT the array containing sequential numbers of atoms to freeze during geometry optimizations and relaxed scans.
- AUTOFV logical flag to automatically fill the FVALUE array using parameters of starting geometry. Default is .true.
- IFDMOD selects one of two programmed methods used to freeze internals in DLCs. IFDMOD=1 is the default. IFDMOD=2 is experimental at present and may not work well in all situations.
- SCAN logical flag used to signal relaxed scans in DLCs. Default is .false.
- DLCTOL tolerance/threshold used to check the quality/completeness of DLCs during DLC generation. Default is DLCTOL=1.0D-5. One may need to lower it to e.g. 1.0D-6 in some rare cases.
- ORTTOL tolerance/threshold used to check the quality/completeness of DLCs after imposing geometry constrains. Default is ORTTOL=1.0D-5. One may need to lower it to up to e.g. 1.0D-8 and below in some cases (e.g., when getting Unable to project DLC error message).
- FRATTL tolerance/threshold used to check the quality/completeness of constrains generated to freeze atoms specified in the IFRZAT array. Default is FRATTL=1.0D-5. One may need to lower it to up to e.g. 1.0D-7 in some cases.
- CNVTOL maximum allowed error for conversion of internals to Cartesians. Default is CNVTOL=1.0D-8. One may need to increase it to e.g. 1.0D-7 in some pathological cases.
- TORTOL threshold value (in radians) to forcibly equate torsions and Out of PLane bends (OPLs) to zero or Pi (for torsions) and ± Pi/2 (for OPLs) if they are close enough to these values (i.e., the difference is less than TORTOL). Default is TORTOL=0.0D0
- OPLTHR threshold (in degrees) used to replace torsions of absolute value larger than OPLTHR by the corresponding OPLs to improve the quality of DLCs. Default is OPLTHR=150.0D0
- DELANG threshold (in degrees) to delete ill-defined anges (i.e., that are larger than DELANG). Default is DELANG=178.0D0
- DELTOR threshold (in degrees) to delete ill-defined torsions (i.e. those that are larger than DELTOR by absolute value). Default is DELTOR=172.0D0. Also affects deletion of ill-defined OPLs (i.e., those that are larger than DELTOR/2 by absolute value).
- STRICT logical flag to delete some extra torsions and OPLs from DLCs. Default is .false.
- STPMAX the value of maximum step size used during conversion of internals to Cartesians. Default is STPMAX=0.50D0. One can try to decrease it to e.g. STPMAX=0.250D0 or below if conversion routine diverges.
- UNSTABLE logical flag used to force propagation of updated Cartesians from master node to all slave processes. Default is .false. It should be used on some hardware to avoid situations when some instances of parallel Firefly process get different results of conversion that other ones. Use of this flag helps to avoid program hangs or unexpected behavior e.g., if running on cluster of non-all-identical nodes.
- HBOND the maximum possible H-bond length (in Angstrom) for the reference H-O-H H-bond used during automatic generation of hydrogen bonds. The default is 2.1 Angstrom. Setting it to zero or negative value disables this feature altogether so you can resort to the old behavior.
- SYMREP integer that codes symmetry replication options for DLC-related arrays. Namely, if the bit 0 (i.e. 1 in decimal) of SYMREP is set this enforces symmetry replication of IXZMAT data, bit 1 (decimal 2) enforces symmetry replication of IRZMAT data, bit 2 (decimal 4) enforces symmetry replication of IFZMAT/IFRZAT data, and finally bit 3 (decimal 8) enforces symmetry replication of NONVDW array. E.g., SYMREP=9 means 1 (for bit 0) + 8 (for bit 3) (or 0x9 in hex as Firefly now accepts binary (e.g., 0b1001), octal (e.g., 0o11), and hexadecimal (e.g., 0x9) input values) and hence will symmetry replicate IXZMAT and NONVDW arrays. The simplest way to enforce all arrays to be symmetry replicated is to enter SYMREP=-1 i.e. to set all the bits of SYMREP. Default is SYMREP=0 (i.e., no replication at all).
At present, Firefly's DLC code uses and recognizes bonds, angles, torsions, and OPLs. This means that any variable of these types can be frozen or used for geometry scans.
Firefly's DLC code can automatically handle degenerate geometries having three consecutive atoms on the straight line (e.g. like in cyanobenzene). However, if there are four or more consecutive atoms on the straight line one need to define some extra coordinates around them, otherwise automatic generation of DLCs fails. Adding some extra coordinates surrounding frozen primitives can also help in the case of "Unable to project DLCs" message during constrained optimization.
There are several related options found in $statpt group as well. The most important are:
- ITBMAT - number of micro-iterations used to compute the step in Cartesians which corresponds to the desired step in internals. The default is 100 as of Firefly v. 7.1.G
- CNSTOL - maximum allowed error in constraints. Default is CNSTOL=1.0D-8. One may need to increase it to e.g. 1.0D-7 in some pathological cases.
On Fri Dec 11 '09 0:19am, Richard wrote
>Maybe you could list the current set of DLC options so users could try out the new features.
[ This message was edited on Sat Dec 19 '09 at 3:21am by the author ]
Sat Dec 19 '09 3:21am
This message read 2887 times