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Dear prof. Erba,
Have You got any time to look into the source maybe? 
Quite interestingly, I have recently noticed that in some other QC code values for the components change a lot (by up to 60%) from run to run, except for the dipole orientation (when the molecular dipole is aligned with z axis). Is (or could be) the reorientation You are referring to connected with this? Seems like something similar to the struggle fir gauge invariance in NMR calculations...
To clarify better, does the symmetrization correspond to the frequency symmetry (which determines the equal components, e.g., xxyy = xyxy = xyyx, etc. for the static case?
Or is this about the geometrical symmetry (and possible reorientation of the molecule to have the dipole moment along an axis)?
Actually, I have now tried using only the "T"-labeled atoms and got this error:
ERROR **** geometry **** FORMAT ERROR IN INPUT DECK
The files are attached...CS2_B1WC.pob_tzvp_rev2_gamma_onlyT.out CS2_B1WC.pob_tzvp_rev2_gamma_bothTandF.out
Dear fbodo,
fbodo said in Unexpectedly cannot get the geometry after optimization: KEYWORD EXTPRT NOT ALLOWED:
In this example you'll have to extract from the second geometry print (i.e. Crystallographic cell) the a and c lattice parameters, given the Tetragonal lattice, alongside the fractionary coordinate of atoms 1 and 3.
Should I only take the atoms labelled by "T" if the lattice is tetragonal, and which ones are to be taken in case of an orthorombic one? Or does "T"'and "F" stand just for "TRUE"'and "FALSE"?
fbodo said in Unexpectedly cannot get the geometry after optimization: KEYWORD EXTPRT NOT ALLOWED:
I don't have your script,
I am actually talking about the standard runPcry23 script. Perhaps it should not be like that? Or should I modify this script?
Thank You for Your help this far!
Yours sincerely,
Igors Mihailovs
Dear developers and others.
I am a bit confused about the output of the second hyperpolarizability calculation:
*******************************************************************************
SECOND HYPERPOLARIZABILITY (GAMMA) TENSOR
COMPONENT GAMMA
*******************************************************************************
XXXX 1.0077E+04 ( 1.0077E+04)
XXXY 4.1650E-13 ( 1.9458E-08)
XXXZ 5.9072E-13 ( 2.5339E-08)
XXYY 3.9702E+03 ( 3.9702E+03)
XXYZ -1.0917E+03 ( -1.0917E+03)
XXZZ 3.2158E+03 ( 3.2158E+03)
XYYY 7.0166E-13 ( 1.4903E-07)
XYYZ 5.2035E-14 ( 2.4139E-08)
XYZZ 1.9596E-13 ( 1.3356E-08)
XZZZ 6.7898E-13 ( -7.7814E-09)
YYYY 7.2247E+03 ( 7.2247E+03)
YYYZ -4.5162E+02 ( -4.5162E+02)
YYZZ 3.0331E+03 ( 3.0331E+03)
YZZZ -1.5476E+01 ( -1.5476E+01)
ZZZZ 1.1089E+04 ( 1.1089E+04)
What are the quantities in parentheses? Are these a result of some rotation? If so, then why only the minor components change? Which ones are the real ones I should use?
Thank You in advance.
I have actually managed to get the crystallographic cell parameters and fractional coordinates, and the calculation seems to be proceeding fine (forces are not greater than 10^-15 a.u.). If anyone finds this useful, the bash script is below. But I haven't tested it with any other spacegroup yet, just the 64th one.
#!/bin/bash
outfile="$1"
[ ! -f "$outfile" ] && echo "File not found!" && exit 5
[ -z "$(grep -e 'FINAL OPTIMIZED GEOMETRY' "$outfile")" ] && echo "The geometry optimization did not finish!" && exit 3
cat "$outfile" | sed -n '/^ *FINAL OPTIMIZED GEOMETRY/,/TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT END/p' | grep -A 2 -e '^ *CRYSTALLOGRAPHIC CELL' | tail -1 | sed 's@ \+@\n@g' | uniq | grep -v -e '^ *$' -e '^90.0000' > "${outfile%out}gem"
fractionals="$(cat "$outfile" | sed -n '/^ *FINAL OPTIMIZED GEOMETRY/,/TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT END/p' | sed -n '/^ *COORDINATES IN THE CRYSTALLOGRAPHIC CELL/,/^ *$/p' | sed '1,3d;$d')"
echo "$fractionals" | wc -l >> "${outfile%out}gem"
echo "$fractionals" | gawk '{printf " %2d\t% 2.12e\t% 2.12e\t% 2.12e\n",$3,$5,$6,$7}' >> "${outfile%out}gem"
Also, in the output file there is this section:
INFORMATION **** fort.34 **** GEOMETRY OUTPUT FILE
DIRECT LATTICE VECTORS CARTESIAN COMPONENTS (ANGSTROM)
X Y Z
0.318445490153E+01 0.274749634689E+01 0.000000000000E+00
-0.318445490153E+01 0.274749634689E+01 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.960489760492E+01
CARTESIAN COORDINATES - PRIMITIVE CELL
*******************************************************************************
* ATOM X(ANGSTROM) Y(ANGSTROM) Z(ANGSTROM)
*******************************************************************************
1 6 C 0.000000000000E+00 0.000000000000E+00 4.802448802459E+00
2 6 C 0.000000000000E+00 2.747496346893E+00 0.000000000000E+00
3 16 S 1.466783675769E-16 1.681580223141E+00 1.145333715792E+00
4 16 S 1.184807688651E-16 1.065916123752E+00 -3.657115086666E+00
5 16 S -5.829198876290E-17 -1.681580223141E+00 -1.145333715792E+00
6 16 S 1.753501641235E-16 -1.065916123752E+00 3.657115086666E+00
**** 8 SYMMOPS - TRANSLATORS IN FRACTIONAL UNITS
**** MATRICES AND TRANSLATORS IN THE CRYSTALLOGRAPHIC REFERENCE FRAME
V INV ROTATION MATRICES TRANSLATORS
1 1 1.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
2 2 -1.00 -0.00 0.00 -0.00 -1.00 0.00 0.00 0.00 1.00 0.50 0.50 0.50
3 3 -0.00 -1.00 0.00 -1.00 -0.00 0.00 0.00 0.00 -1.00 0.00 0.00 0.00
4 4 0.00 1.00 0.00 1.00 0.00 0.00 0.00 0.00 -1.00 0.50 -0.50 0.50
5 5 -1.00 -0.00 0.00 -0.00 -1.00 0.00 0.00 0.00 -1.00 0.00 0.00 0.00
6 6 1.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 -1.00 0.50 -0.50 0.50
7 7 0.00 1.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
8 8 -0.00 -1.00 0.00 -1.00 -0.00 0.00 0.00 0.00 1.00 0.50 0.50 0.50
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT END TELAPSE 1827.53 TCPU 1820.59
EEEEEEEEEE TERMINATION DATE 13 08 2025 TIME 11:14:46.6
If I just copy it with *.f34 extension, would that be equivalent to the fort.34 file?
Dear Giacomo Ambrogio,
Now I have moved the EXTPRT keyword, and the job did run. However, runPcry23 script did not indeed copy fort.34 file back to the launch directory. This is despite that runPcry23 -h suggests it should indeed copy it. Are there any workarounds to persuade the script to actually copy the fort.34 file?
About the manual extraction – do I understand correctly that I should take the primitive and not crystallographic cell parameters?! The input in the .d12 file is in crystallographic cell, isn't it?
Also, I am a bit confused as to why in the input at the beginning there were only 2 fractional coordinates, but in the end the results of the geometry optimization show 6 fractional coordinates?
Dear CRYSTAL support and others,
I am new to CRYSTAL, hence the error is probably on my side.
I am trying to perform a geometry optimization of a molecular crystal and then use it to compute the dielectric susceptibilities. If I understand it correctly, I need to use the keyword EXTPRT within the OPTGEOM section to export the optimized geometry and get a fort.34 file, which I then have to use in my next calculation with EXTERNAL keyword for the geometry.
However, the run fails with an error message:
ERROR **** CONOPT_ **** KEYWORD EXTPRT NOT ALLOWED
forrtl: error (78): process killed (SIGTERM)
If I remove the EXTPRT keyword, the optimization runs just fine (at least with some of the functionals)! But I cannot get the geometry out of the .OUT file. I tried using the cell parameters I got after "CRYSTALLOGRAPHIC CELL" and run an elastic constant calculation; however, it failed with "WARNING!! FORCE 9 AT CENTRAL POINT IS GREATER THAN 10^-4. OPTIMIZE THE STRUCTURE AND RE-RUN" (there were multiple such messages for multiple force vectors) and the error
ERROR **** BFGS_ **** PXK TOO SMALL
So I am now at loss trying to get the geometry out of my optimization. Can anyone help please?
Please find inputs for the jobs attached.
CS2_normalP_r2SCANh.pob_tzvp_rev2_opt_withEXTPRT.out CS2_normalP_r2SCANh.pob_tzvp_rev2_opt_withoutEXTPRT.out CS2_r2SCANh.pob_tzvp_rev2_elconst_manualCOORDS.out
We are researching LiF and we are interested in creating a potential energy curve for the crystalline structure of LiF. From what we have already found out, a diatomic case is not described in an asymptotically correct way by any density functional but is described by MP2–MP4 (the internal energy with Coulomb energy subtracted goes to 0 at large distances).
In the manual, it is mentioned that CRYSTAL can compute MP2 for single points. However, when we launch it, the following error happens:
We tried both the parallel and the serial version, the error is the same. Actually, for the parallel version it starts to compute MP2 and then falls out.
What can be the issue?