2014-12-02 9:53 GMT-07:00 Vitalie Botan <[email protected]>: > > > On Tuesday, December 2, 2014 4:47:22 PM UTC+1, Christoph Junghans wrote: >> >> 2014-12-01 18:11 GMT-07:00 Vitalie Botan <[email protected]>: >> >> Most of the code is already there, it is just not enabled, because I >> have never used tabulated bonded interaction in LAMMPS. >> Do you have a specification for LAMMPS' bonded tables? (i.e. what's >> in the 1st, 2nd, 3rd column for bond, angle and dihedral tables?) > > > Hi Christoph, > > Thanks for the prompt reply, it seems I overlooked the fact, that gromacs > version of the script produces not only xvg-table, but a normal one as well. > Regarding the format of the bonded tabulated potential, it is very similar > to the non-bonded format (which is already implemented in votca) with few > exceptions I have copied from the Lammps manual below: > > 1) A section begins with a non-blank line whose 1st character is not a "#"; > blank lines or lines starting with "#" can be used as comments between > sections. The first line begins with a keyword which identifies the section. > The next line lists (in any order) one or more parameters for the table. > Each parameter is a keyword followed by one or more numeric values. The > parameter "N" is required and its value is the number of table entries that > follow. Following a blank line, the next N lines list the tabulated values. > On each line, the 1st value is the index from 1 to N, the 2nd value is the > bond length r (in distance units), the 3rd value is the energy (in energy > units), and the 4th is the force (in force units). The bond lengths must > range from a LO value to a HI value, and increase from one line to the next. > If the actual bond length is ever smaller than the LO value or larger than > the HI value, then the bond energy and force is evaluated as if the bond > were the LO or HI length. > 2) For angle potential, on each line, the 1st value is the index from 1 to > N, the 2nd value is the angle value (in degrees), the 3rd value is the > energy (in energy units), and the 4th is -dE/d(theta) (also in energy > units). The 3rd term is the energy of the 3-atom configuration for the > specified angle. The last term is the derivative of the energy with respect > to the angle (in degrees, not radians). Thus the units of the last term are > still energy, not force. The angle values must increase from one line to the > next. The angle values must also begin with 0.0 and end with 180.0, i.e. > span the full range of possible angles. > 3) For dihedral potential, on each line, the 1st value is the index from 1 > to N, the 2nd value is the angle value, the 3rd value is the energy (in > energy units), and the 4th is -dE/d(phi) also in energy units). The 3rd term > is the energy of the 4-atom configuration for the specified angle. The 4th > term (when present) is the negative derivative of the energy with respect to > the angle (in degrees, or radians depending on whether the user selected > DEGREES or RADIANS). Thus the units of the last term are still energy, not > force. The dihedral angle values must increase from one line to the next. > > Dihedral table splines are cyclic. There is no discontinuity at 180 degrees > (or at any other angle). In general, the first angle in the list can have > any value (positive, zero, or negative). However the range of angles > represented in the table must be strictly less than 360 degrees (2pi > radians) to avoid angle overlap. (You may not supply entries in the table > for both 180 and -180, for example.) If the user's table covers only a > narrow range of dihedral angles, strange numerical behavior can occur in the > large remaining gap. > > Hope these restrictions don't pose any problem for implementing in the > script. Thanks in advance. I hacked something together quickly: <https://code.google.com/p/votca/source/detail?r=1e124eb53c82c3fd451e08f57065ac10ec17eb4f&repo=csg> Dihedral tables aren't support in their full beauty yet, but also for Gromacs the periodicity of the table is not imposed.
Christoph > > Best, > > --Vitalie > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
