lmmentel / chemtools Goto Github PK
View Code? Open in Web Editor NEWPython tools for quantum chemical calculations
License: MIT License
Python tools for quantum chemical calculations
License: MIT License
Hi!
I installed chemtools with pip:
chemtools 0.9.2
I have a GAMESS-US file which looks like this:
$DATA
CARBON
S 9
1 0.051344 0.013991
2 0.102619 0.169852
3 0.205100 0.397529
4 0.409924 0.380369
5 0.819297 0.180113
6 1.637494 -0.033512
7 3.272791 -0.121499
8 6.541187 0.015176
9 13.073594 -0.000705
P 9
1 0.029281 0.001787
2 0.058547 0.050426
3 0.117063 0.191634
4 0.234064 0.302667
5 0.468003 0.289868
6 0.935757 0.210979
7 1.871016 0.112024
8 3.741035 0.054425
9 7.480076 0.021931
BORON
S 9
1 0.040569 0.032031
2 0.081044 0.243317
3 0.161898 0.434636
4 0.323418 0.329581
5 0.646080 0.111875
6 1.290648 -0.078699
7 2.578276 -0.098781
8 5.150520 0.016164
9 10.288990 -0.000016
S 1
1 0.082968 1.000000
S 1
1 0.305133 1.000000
S 1
1 0.422217 1.000000
P 9
1 0.029207 0.019909
2 0.058408 0.141775
3 0.116803 0.294463
4 0.233582 0.309028
5 0.467115 0.236378
6 0.934132 0.131317
7 1.868068 0.066454
8 3.735743 0.021248
9 7.470701 0.002837
$END
when I run
from chemtools.basisset import BasisSet
print(basis["B"])
I get the list of exponents reversed, but not the coefficients:
Name = test_file
Element = B
Family = None
Kind = None
Functions:
================s shell=================
Contracted:
1 10.2889900000 0.03203100
2 5.1505200000 0.24331700
3 2.5782760000 0.43463600
4 1.2906480000 0.32958100
5 0.6460800000 0.11187500
6 0.3234180000 -0.07869900
7 0.1618980000 -0.09878100
8 0.0810440000 0.01616400
9 0.0405690000 -0.00001600
Uncontracted:
10 0.0829680000 1.00000000
11 0.3051330000 1.00000000
12 0.4222170000 1.00000000
================p shell=================
Contracted:
1 0.0292070000 0.01990900
2 0.0584080000 0.14177500
3 0.1168030000 0.29446300
4 0.2335820000 0.30902800
5 0.4671150000 0.23637800
6 0.9341320000 0.13131700
7 1.8680680000 0.06645400
8 3.7357430000 0.02124800
9 7.4707010000 0.00283700
It could be related to a sort that happens in the list of exponents...
I've noticed that in parse_gaussian_basis the regular expression has an issue.
shellre = re.compile(r'^\s*(?P[SPDFGHILspdfghil]+)\s*(?P[1-9]+)\s*(?P-?\d+.\d+)')
I think should be
shellre = re.compile(r'^\s*(?P[SPDFGHILspdfghil]+)\s*(?P[0-9]+)\s*(?P-?\d+.\d+)')
That fixes the problem for me. Basis sets with 10 exponents are now accepted.
I was trying to branch and pull request but I'm new to git and can't seem to figure it out.
Tobias
Hi, Dr. Mentel. I have used 'pip' to install your chemtools and the program to read two-electrons integrals from Gamess-us. I have followed your tutorial, but there are some questions. Firstly, the modules 'gamessreader' and 'gamessus' are in the calculators floder, but there are 'from chemtools.gamessreader' and 'from chemtools.gamessus'. So, I have changed my python program based on your tutorial. When I run my python program, it will get '.F' files, however, it will be a new error which says name 'twoe' is not defined. The 'twoe' is in the module gamessreader.py.I have put my python program which I wrote following your tutorial, bash script and error.out in the appendix. Please find them attached. It will be appreciated to hear from you asap.
run.sh.txt
twoint.py.txt
Use of Gamess wrapper impossible on Linux machines due to chemtools providing an invalid command to the shell resulting in a DDI error and failed computation. Could you rework get_command module to provide a proper command as in pygamess:
exec_string = "{0} {1} {2} -ddi {3} {3} {4} -scr {5} > {6}".format(ddikick, gamess, self.jobname, self.num_cores, hostname, self.tempdir, self.gamout)
where ddikick is a path to DDI, gamess is a path to executable, self.jobname is an input file, num_cores is a number of cores, self.tempdir is a scratch folder, and self.gamout is an output file.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.