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项目作者： grimme-lab

项目描述 ：
sTDA-xTB Hamiltonian for ground state
高级语言： Fortran
项目地址: git://github.com/grimme-lab/xtb4stda.git
创建时间： 2019-11-27T12:03:12Z
项目社区：https://github.com/grimme-lab/xtb4stda
开源协议：GNU Lesser General Public License v3.0
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sTDA-xTB for ground state calculations

Build Status
Build Status

This project provides xtb4stda, a program to calculate the ground state with
sTDA-xTB to be used in further stda
calculations.

Installation

Statically linked binaries can be found at the projects
release page.
To build from source this project uses a make based build system and requires
a version of Intel Parallel Studio 17 or newer to be compiled (also requires
ruby for some hacky scripts).
To trigger the build run in the root directory

  1. make

You will find a statically linked executable in exe/xtb4stda.
To make xtb4stda accessible export

  1. export XTB4STDAHOME=$PWD
  2. export PATH=$PATH:XTB4STDAHOME/exe

For parallel usage set the threads for OMP and the MKL linear algebra backend by

  1. export OMP_NUM_THREADS=<ncores> MKL_NUM_THREADS=<ncores>

For larger systems please adjust the stack size accordingly, otherwise
stack overflows will occur. Use something along the lines of this:

  1. ulimit -s unlimited
  2. export OMP_STACKSIZE=4G

To make adjustments to the build system check the directory MAKE/.

Alternatives

If you are not a fan of make, you can use meson
as alternative, but it requires a fairly new version like 0.49 or newer for a
decent Fortran support.
For the default backend ninja version 1.5 or newer
has to be provided.

To perform a build run (with GCC, run export FC=ifort for Intel builds)

  1. meson setup build_gcc
  2. ninja -C build_gcc

This also allows to install the program locally by running

  1. [sudo] ninja -C build_gcc install

Which will default to an installation in /usr/local and should automatically
include xtb4stda in your systems PATH variable.
The environment variable to set is than usually only

  1. export XTB4STDAHOME=/usr/local/share/xtb4stda

Usage

The xtb4stda binary will read the geometry from its first command line argument
and the input is assumed to be either a Turbomole coordinate data group or a
xyz-file. The extension of the file is not used to distinguish files.

  1. xtb4stda coord > gs.stda-xtb.out

After the run you will find a wfn.xtb file in the directory which can be used
with the stda program.

Citations

  • S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
    DOI: 10.1063/1.4959605

License

xtb4stda is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

xtb4stda is distributed in the hope that it will be useful,
but without any warranty; without even the implied warranty of
merchantability or fitness for a particular purpose. See the
GNU Lesser General Public License for more details.

Bugs

A bug is a demonstratable problem caused by the code in this repository.
Good bug reports are extremely valuable for us - thank you!

Before opening a bug report:

  1. Check if the issue has already been reported.
  2. Check if it still is an issue or has already been fixed?
    Try to reproduce it with the latest version from the master branch.
  3. Isolate the problem and create a reduced test case.

A good bug report should not leave others needing to chase you up for more
information. So please try to be as detailed as possible in your report,
answer at least these questions:

  1. Which version of xtb4stda are you using? The current version is always
    a subject to change, so be more specific.
  2. What is your environment (your laptop, the cluster of the university)?
  3. What steps will reproduce the issue?
    We have to reproduce the issue, so we need all the input files.
  4. What would be the expected outcome?
  5. What did you see instead?

All these details will help people to fix any potential bugs.

Known Issues

For large systems with more than 33000 basis functions an integer overflow
in the linear algebra backend will occur. To amend this issue the integer
precision range must be increased from 32 bits to 64 bits by recompiling
the program.
Adjust the make build by changing -lmkl_intel_lp64 to -lmkl_intel_il64
in MAKE/Makerules
or when using the meson backend by adding -Dinterface=64 in the
configuration step.
Note that this option is currently only supported with the MKL backend.