VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Feb 26 2014 - 12:57:44 CST

All,

Massimiliano and I have worked offline to track this bug down. The order of certain keywords we use to parse the Gaussian LOG files were switched for G09RevC and then reverted in G09RevD. I have updated the relevant QMTool code, which should fix the observed issues. These fixes will be incorporated into the next VMD 1.9.2a release. Anyone using G09RevD should use this new code when available, and let me know if any unintended errors crop up.

Regards,
Christopher Mayne


On Feb 25, 2014, at 7:38 PM, Tim Lo wrote:

Dear Masimiliano,

I have experienced a similar problem before too. When I loaded the log files into "Water Int.", my observations were the same as yours.

When I ignored this error and started using "Opt. Charges", the error that I got was a bit different from yours:
can't use empty string as operand of "-"
can't use empty string as operand of "-"
    while executing
"expr {[lindex $y 1]-$T*log(rand())}"
    (procedure "simulated_annealing" line 30)
    invoked from within
"simulated_annealing $T "
    (procedure "::Optimize::Opt1::handle" line 202)
    invoked from within
"$opt start"
    (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 421)
    invoked from within
"::ForceFieldToolKit::ChargeOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
    invoked from within
"::ForceFieldToolKit::gui::coptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt in..."
    (command bound to event)

Then, the TK console said:
Optimization completed. -- Stationary point found.
Optimization completed. -- Stationary point found.
No mulliken charges found.
Optimization completed. -- Stationary point found.
Optimization completed. -- Stationary point found.
No mulliken charges found.
Creating namespace ::Optimize::Opt0
Starting 0-dimensional optimization.
Starting optimization with following simplex:
0: --> 7321.657410393737
Simulated annealing:
Initial temperature T0=25.0
Number of T cycles Tsteps=20
Simulated annealing step 0: T=25.0
Optimization completed. -- Stationary point found.
Optimization completed. -- Stationary point found.
No mulliken charges found.
Optimization completed. -- Stationary point found.
Optimization completed. -- Stationary point found.
No mulliken charges found.
Creating namespace ::Optimize::Opt1
Starting 0-dimensional optimization.
Starting optimization with following simplex:
0: --> 7321.657410393737
Simulated annealing:
Initial temperature T0=25.0
Number of T cycles Tsteps=20
Simulated annealing step 0: T=25.0

I think this error is due to the different keywords/ keyword order used in Gaussian09 Rev. D.01, compared to Gaussian09 Rev. C.01. I solved this problem by using Rev. C.01 to calculate the water interactions. I suggest using Gaussian09 Rev. C.01 to try it again to check if the same error appears again.

Regards,
Tim

On 2014/2/26 上午 06:18, Massimiliano Porrini wrote:
Dear all,

I am experiencing some problems with the valuable ffTK of VMD version 1.9.2a35 .

I could very smoothly reach the step of QM interaction with water molecules.

Indeed, I generated the Gaussian input files for the interaction with the
water molecule, then I ran G09 with them and I successfully obtained
the related log files.

But, in the TAB named "Water Int.", if I try to upload these log
files to check the optimised geometry, the following error message pops up:


Couldn't read 'Input orientation'!


And in the TkConsole the following lines appear (for each .log file I attempted
to upload):


Reading internal coordinates from 'Initial Parameters'.
No 'Initial Parameters' section found!
No cartesian coordinates given in Z-matrix.
Reading 'Input Orientation'.


Besides, in the end, the following message shows up:


list element in quotes followed by "," instead of space
list element in quotes followed by "," instead of space
    while executing
"lindex $line 0"
    (procedure "::QMtool::read_gaussian_log" line 154)
    invoked from within
"::QMtool::read_gaussian_log $logfile $molId"
    ("foreach" body line 5)
    invoked from within
"foreach logfile $::ForceFieldToolKit::gui::gzmLOGfiles {
                    set molId [mol new]
                    ::QMtool::use_vmd_molecule $molId..."
    invoked from within
".fftk_gui.hlf.nb.genzmat.run.loadLOG invoke "
    invoked from within
".fftk_gui.hlf.nb.genzmat.run.loadLOG instate {pressed !disabled} { .fftk_gui.hlf.nb.genzmat.run.loadLOG state !pressed; .fftk_gui.hlf.nb.genzmat.run.l..."
    (command bound to event)


However, if I try to skip this step (which is supposed to be just a visualization check of
the optimised geometries with water) and I use the G09 log files for the Charge Optimisation
step, I get the following error:


atomselect set: 0 data items doesn't match 1 selected atoms.
atomselect set: 0 data items doesn't match 1 selected atoms.
    while executing
"$temp set x [lindex [lindex $molCoords $i] 0]"
    (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 187)
    invoked from within
"::ForceFieldToolKit::ChargeOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
    invoked from within
"::ForceFieldToolKit::gui::coptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt in..."
    (command bound to event)


And in the TkConsole:


Error termination request processed by link 9999.
No mulliken charges found.
No mulliken charges found.
Optimization completed. -- Stationary point found.
Optimization completed. -- Stationary point found.
***
No mulliken charges found.
Error termination via Lnk1e in /r1/software/g09revD01_nehalem/g09/l1.exe at Tue Feb 25 10:25:16 2014.


Has anybody already encountered and hopefully got this(these) issue(s)
sorted out?

Best wishes,


PS If necessary, I might also send off list the "debugging log file" I obtained from this last step.



--
Dr Massimiliano Porrini
Institut Européen de Chimie et Biologie (IECB)
CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
2, rue Robert Escarpit
33607 Pessac Cedex
France
http://www.iecb.u-bordeaux.fr/

Emails: m.porrini_at_iecb.u-bordeaux.fr<mailto:m.porrini_at_iecb.u-bordeaux.fr>
            M.porrini_at_ed.ac.uk<mailto:M.porrini_at_ed.ac.uk>
            maxp_at_iesl.forth.gr<mailto:maxp_at_iesl.forth.gr>
            mozz76_at_gmail.com<mailto:mozz76_at_gmail.com>