Comments (5)
polyluxus
commented on June 9, 2024
Prepare will now filter the route section for a comment before applying it (at least currently for the -R/-l switches.
$ g16.prepare.dev -llist
INFO : Configuration file '<HOME>/devel/tools-for-g16.bash/.g16.toolsrc' applied.
0 : # PM6
1 : #P B97D3/def2SVP/W06 DenFit
2 : #P B97D3/def2TZVPP/W06 DenFit
3 : #P PBE1PBE/def2SVP ! this is known as pbe0
$ g16.prepare.dev -l3 -ropt -jtest start.xyz
INFO : Configuration file '<HOME>/devel/tools-for-g16.bash/.g16.toolsrc' applied.
INFO : Removed comment: this is known as pbe0
INFO : Applied route section:
INFO : #P PBE1PBE/def2SVP
INFO : Added 'opt' to the route section.
INFO : Setting charge (0) and multiplicity (1).
INFO : Using caption 'Calculation: test; chrg 0; mult 1; uhf 0; 2019-04-16 20:53:28 (CEST)'.
INFO : Checkpoint file 'test.chk' does not exists and will be created.
INFO : Added 'MaxDisk=30000MB' to the route section.
INFO : Written modified inputfile 'test.com'.
INFO : g16.prepare.sh is part of tools-for-g16.bash 0.3.0.dev (2019-04-XX)
$ head -n5 test.com
%Chk=test.chk
%NProcShared=12
%Mem=4000MB
#P PBE1PBE/def2SVP opt MaxDisk=30000MB
This allows the following in the .g16.toolsrc:
# Predefined Route sections
g16_route_section_default="#P B97D3/def2SVP/W06 DenFit"
g16_route_section_predefined[0]="# PM6"
g16_route_section_predefined[1]="#P B97D3/def2SVP/W06 DenFit"
g16_route_section_predefined[2]="#P B97D3/def2TZVPP/W06 DenFit"
g16_route_section_predefined[3]="#P PBE1PBE/def2SVP ! this is known as pbe0"
#
What remains now is building this section ...
Note though:
$ g16.prepare.dev -R'#P PBE1PBE/def2SVP ! this is known as pbe0' -ropt -jtest start.xyz
INFO : Configuration file '<HOME>/devel/tools-for-g16.bash/.g16.toolsrc' applied.
INFO : Removed comment: this is known as pbe0
INFO : Route section has no syntax errors.
INFO : Applied route section:
INFO : #P PBE1PBE/def2SVP
INFO : Added 'opt' to the route section.
INFO : Setting charge (0) and multiplicity (1).
INFO : Using caption 'Calculation: test; chrg 0; mult 1; uhf 0; 2019-04-16 20:57:53 (CEST)'.
INFO : Checkpoint file 'test.chk' does not exists and will be created.
INFO : Added 'MaxDisk=30000MB' to the route section.
INFO : Written modified inputfile 'test.com'.
INFO : g16.prepare.sh is part of tools-for-g16.bash 0.3.0.dev (2019-04-XX)
$ tail -n3 test.com
!Automagically created with g16.prepare.sh (tools-for-g16.bash, 0.3.0.dev, 2019-04-XX)
!'<HOME>/bin/g16.prepare.dev' '-R#P PBE1PBE/def2SVP ! this is known as pbe0' '-ropt' '-jtest' 'start.xyz'
The comment will still be saved.
from tools-for-g16.bash.
O2-AC
commented on June 9, 2024
Not sure if that is overcomplicating the problem, but instead of saving the comment to a predefined route section in that variable itself, one could think about a new variable g16_route_section_predefined_comment[n] with n corresponding to the respective g16_route_section_predefined[n].
In that case only the output of g16.prepare -l list would need to be changed to concatenate the respective comment to the predefined route section. All the other scripts could stay as they are. This would also allow for a nicer formatting with line breaks in the output of g16.prepare -l list.
from tools-for-g16.bash.
polyluxus
commented on June 9, 2024
Not sure if that is overcomplicating the problem, but instead of saving the comment to a predefined route section in that variable itself, one could think about a new variable
g16_route_section_predefined_comment[n]withncorresponding to the respectiveg16_route_section_predefined[n].
That is now part of the prepare script, but still needs a lot of manual labour.
$ g16.prepare.dev -llist
INFO : Configuration file '<HOME>/devel/tools-for-g16.bash/g16.tools.rc' applied.
0 : # PM6
0(cmt.) : semi-empirical method (default route)
1 : #P B97D3/def2SVP/W06 DenFit
1(cmt.) : pure DFT method with density-fitting, double zeta BS (default route)
2 : #P B97D3/def2TZVPP/W06 DenFit
2(cmt.) : pure DFT method with density-fitting, triple zeta BS (default route)
3 : #P BP86/def2SVP/W06 EmpiricalDispersion=GD3BJ DenFit
3(cmt.) : pure DFT method with density-fitting and DFT-D3 with Becke-Johnson damping,
3(cmt.) : double zeta BS (default route)
4 : #P BP86/def2TZVPP/W06 EmpiricalDispersion=GD3BJ DenFit
4(cmt.) : pure DFT method with density-fitting and DFT-D3 with Becke-Johnson damping,
4(cmt.) : triple zeta BS (default route)
5 : #P PBE1PBE/def2SVP EmpiricalDispersion=GD3BJ
5(cmt.) : hybrid DFT method with DFT-D3 with Becke-Johnson damping, double zeta BS
5(cmt.) : (default route)
6 : #P PBE1PBE/def2TZVPP EmpiricalDispersion=GD3BJ
6(cmt.) : hybrid DFT method with DFT-D3 with Becke-Johnson damping, triple zeta BS
6(cmt.) : (default route)
7 : #P B3LYP/def2SVP EmpiricalDispersion=GD3BJ
7(cmt.) : hybrid DFT method with DFT-D3 with Becke-Johnson damping, double zeta BS
7(cmt.) : (default route)
8 : #P B3LYP/def2TZVPP EmpiricalDispersion=GD3BJ
8(cmt.) : hybrid DFT method with DFT-D3 with Becke-Johnson damping, triple zeta BS
8(cmt.) : (default route)
from tools-for-g16.bash.
polyluxus
commented on June 9, 2024
I think for the most part this is working now:
path/to/configure.sh -R
will load the configuration file in the same behaviour as the main scripts, then will jump to the route builder, which will cause the routebuilder.sh script to be loaded. (Yes, I know that is a bit complicated, but I did not see how to prevent this. routebuilder.sh has very limited utility as a standalone script.)
Finally, it will replace the found configuration file (maintaining a backup as usual).
What is missing so far is, that entered route sections will be checked, but I need to think about how to return to the editor window, if there are syntax errors, including the actual error so that the user gets a hint where it failed.
from tools-for-g16.bash.
polyluxus
commented on June 9, 2024
What is missing so far is, that entered route sections will be checked, but I need to think about how to return to the editor window, if there are syntax errors, including the actual error so that the user gets a hint where it failed.
This should now work in some fashion. It will not take you back to the edit screen, but if an error is detected, it will amend the comment with a warning.
$ ./routebuilder.sh
INFO : Configuration file '<HOME>/devel/tools-for-g16.bash/configure/.g16.toolsrc' applied.
0 : # PM6
0(cmt.) : semi-empirical method (default route)
1 : #P B97D3/def2SVP/W06 DenFit
1(cmt.) : pure DFT method with dens. fitting and with DFT-D3 (Becke-Johnson damping),
1(cmt.) : double zeta BS
2 : #P B97D3/def2TZVPP/W06 DenFit
2(cmt.) : pure DFT method with dens. fitting and with DFT-D3 (Becke-Johnson damping),
2(cmt.) : triple zeta BS
INFO : Which route section would you like to edit?
INFO : To create a new route section pick an unused number.
INFO : To delete a route section suffix/append 'd' to its index number.
INFO : Enter 's' save the manipulated data to '/tmp/tmp.kgCpJfsUqm'.
INFO : Please enter an integer value or 'q' to quit.
ANSWER : 0
This feature is not yet fully implemented.
WARNING : There was an error in the route section
INFO : Loading CHEMISTRY environment [ OK ]
INFO : Loading gaussian/16.b01_bin [ OK ]
INFO : (External Revision) ES64L-G16RevB.01 20-Dec-2017 NErtGn=2000 NextEG=1161 MaxAtm=250000 MDCach=131072
INFO : -------
INFO : # PM666
INFO : -------
INFO : QPErr --- A syntax error was detected in the input line.
INFO : # PM666
INFO : '
INFO : Last state= "GCL"
INFO : TCursr= 3939 LCursr= 2
INFO : Error termination via Lnk1e at Sat May 18 18:02:45 2019.
0 : # PM666
0(cmt.) : (WARNING: Syntax error detected.) semi-empirical method (devil route)
1 : #P B97D3/def2SVP/W06 DenFit
1(cmt.) : pure DFT method with dens. fitting and with DFT-D3 (Becke-Johnson damping),
1(cmt.) : double zeta BS
2 : #P B97D3/def2TZVPP/W06 DenFit
2(cmt.) : pure DFT method with dens. fitting and with DFT-D3 (Becke-Johnson damping),
2(cmt.) : triple zeta BS
INFO : Which route section would you like to edit?
INFO : To create a new route section pick an unused number.
INFO : To delete a route section suffix/append 'd' to its index number.
INFO : Enter 's' save the manipulated data to '/tmp/tmp.kgCpJfsUqm'.
INFO : Please enter an integer value or 'q' to quit.
ANSWER : q
from tools-for-g16.bash.
Related Issues (20)
- Language formatting needs to be checked
- configure has a few problems writing all correct values to file HOT 1
- Add `--` to terminate reading options. HOT 2
- g16.prepare -u switch doesn't exit properly, some values not accepted
- all input scripts need '-f' switch
- Add new queue: SLURM HOT 1
- validate_g16_route missing in spinput, but is referred to
- submit mangles link0 directives into the body of the input file HOT 1
- g16.spinput -R switch has no effect
- Input geometry with fragment specifications is not recognised be g16.prepare HOT 2
- Seemingly empty route sections are not detected
- Support different duration values for the script
- Wrong duration will not exit script
- Typo in g16.submit output HOT 1
- Version warning fires on false positive
- Recursive mode for g16.chk2xyz HOT 1
- configure script buggy in translate mode (-T switch) HOT 1
- Wrong check for profile HOT 1
- Language reset not sufficient
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from tools-for-g16.bash.