tilde-lab/pycrystal

Utilities for ab initio modeling suite CRYSTAL, developed in Turin University

pycrystal's Issues

parser obtaining wrong tot. energy value

If the geometry optimization is completed in one step, the parser receives an energy value that does not include dispersion energy (d3).
Here is an example of *.out file.
ws2nt84_66.log

Gaussian basis set handling is distributed (and re-implemented) across 3 different spots

We have a major design issue here, the three different code parts deal with more or less the same:

• pycrystal.CRYSTOUT.parse_bs_input - cumbersome code of mine, but deals with GHOST, d12 / out format
• pycrystal.parse_bs - old legacy code by @mlosev, but useful for dealing with GAUSSIAN / EMSL format
• aiida_crystal_dft.io.parsers.gto_basis_parser - concise code by @ansobolev, but too general

Skipped conversion to eV?

# dealing with Fermi energies
state_dict['e_fermi'] = float(self.patterns['e_fermi'].search(self.data).groups()[0])
state_dict['e_fermi_units'] = 'Ha'

* Hartree ?

Phonon-related properties to be extracted

• polarizability (alpha(re, im)), dielectric (epsilon(re, im)) and first-order electric susceptibility (chi(1)) tensors (independent components)

• first hyperpolarizability (beta) and second electric susceptibility (chi(2)) tensors (independent components)

• second hyperpolarizability (gamma) and third electric susceptibility (chi(3)) tensors

CVE-2021-34141 (Medium) detected in numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl

CVE-2021-34141 - Medium Severity Vulnerability

Vulnerable Library - numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl

NumPy is the fundamental package for array computing with Python.

Library home page: https://files.pythonhosted.org/packages/6d/ad/ff3b21ebfe79a4d25b4a4f8e5cf9fd44a204adb6b33c09010f566f51027a/numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl

Path to dependency file: /requirements.txt

Path to vulnerable library: /requirements.txt,/requirements.txt

Dependency Hierarchy:

• ❌ numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (Vulnerable Library)

Found in HEAD commit: 65fd1d33fb4108677a14960e522f7ed781cbf4c9

Found in base branch: master

Vulnerability Details

An incomplete string comparison in the numpy.core component in NumPy before 1.22.0 allows attackers to trigger slightly incorrect copying by constructing specific string objects. NOTE: the vendor states that this reported code behavior is "completely harmless."
Mend Note: After conducting further research, Mend has determined that versions 1.12.0 through 1.21.6 of numpy are vulnerable to CVE-2021-34141

Publish Date: 2021-12-17

URL: CVE-2021-34141

CVSS 3 Score Details (5.3)

Base Score Metrics:

• Exploitability Metrics:
  • Attack Vector: Network
  • Attack Complexity: Low
  • Privileges Required: None
  • User Interaction: None
  • Scope: Unchanged
• Impact Metrics:
  • Confidentiality Impact: None
  • Integrity Impact: None
  • Availability Impact: Low

For more information on CVSS3 Scores, click here.

Suggested Fix

Type: Upgrade version

Origin: https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2021-34141

Release Date: 2021-12-17

Fix Resolution: 1.22.0

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Problematic basis sets found inside Unito CRYSTAL library

        # NB. Hg and Bi have unexpected comments
        # NB. Tl has wrong INPUT
        # NB. sometimes the comments get included afterwards

Consider auto-downloading of the CRYSTAL tests

https://www.crystal.unito.it/test_cases/test_cases_inp-out_CRY17.tgz

CVE-2019-6446 High Severity Vulnerability detected by WhiteSource

CVE-2019-6446 - High Severity Vulnerability

Vulnerable Library - numpy-1.16.1-cp35-cp35m-manylinux1_x86_64.whl

NumPy is the fundamental package for array computing with Python.

path: /tmp/git/pycrystal/requirements.txt,/tmp/git/pycrystal

Library home page: https://files.pythonhosted.org/packages/ad/15/690c13ae714e156491392cdbdbf41b485d23c285aa698239a67f7cfc9e0a/numpy-1.16.1-cp35-cp35m-manylinux1_x86_64.whl

Dependency Hierarchy:

• ase-3.16.2-py3-none-any.whl (Root Library)
  • ❌ numpy-1.16.1-cp35-cp35m-manylinux1_x86_64.whl (Vulnerable Library)

Vulnerability Details

An issue was discovered in NumPy 1.16.0 and earlier. It uses the pickle Python module unsafely, which allows remote attackers to execute arbitrary code via a crafted serialized object, as demonstrated by a numpy.load call.

Publish Date: 2019-01-16

URL: CVE-2019-6446

CVSS 3 Score Details (9.8)

Base Score Metrics:

• Exploitability Metrics:
  • Attack Vector: Network
  • Attack Complexity: Low
  • Privileges Required: None
  • User Interaction: None
  • Scope: Unchanged
• Impact Metrics:
  • Confidentiality Impact: High
  • Integrity Impact: High
  • Availability Impact: High

For more information on CVSS3 Scores, click here.

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Elastcon parsing error

/root/.aiida/repository-default/repository/node/39/69/1198-d9f2-48df-815a-3a85a640a599/path/_scheduler-stderr.txt unexpected CRYSTOUT parser error in /root/.aiida/repository-default/repository/node/39/69/1198-d9f2-48df-815a-3a85a640a599/path/_scheduler-stderr.txt:
 Traceback (most recent call last):
  File "/root/tilde/tilde/core/api.py", line 280, in _parse
    for calc in self.Parsers[parser_name].iparse(parsable):
  File "/root/tilde/tilde/parsers/__init__.py", line 117, in iparse
    return [cls(filename)]
  File "/root/tilde/tilde/parsers/CRYSTAL/CRYSTAL.py", line 17, in __init__
    result = _CRYSTOUT(filename)
  File "/usr/local/lib/python3.5/dist-packages/pycrystal/output.py", line 283, in __init__
    self.info['elastic']['elastic_moduli'] = self.get_elastic('elastic_moduli')
  File "/usr/local/lib/python3.5/dist-packages/pycrystal/output.py", line 785, in get_elastic
    constants[-1].append(float(ec))
ValueError: could not convert string to float: '178.7547-193.8748'

NaNs are treated differently in parser code

Should we throw them away or keep?

Parser does not get the correct length of translation vectors

The parser has a limitation on the length of the translation vectors of 50 angstroms, making serious difficulties in case one-dimensional objects when the vector a length can exceed this value. Can you fix it?