Thom Group Wiki - User contributions [en]

Parsing a QChem Output File

2026-04-01T17:12:55Z

Jst55:

__TOC__

==Summary==
To extract all data from a QChem output file, you can use the QChemParser object from <pre>qcmagic.interfaces.parsers.qchem_parser.qchem_parser</pre>
Parsing is not automatic, you first have to create a parser object
<pre>parser = QChemParser('/path/to/file.out')</pre>
The actual parsing occurs when you call the parser object with a list of sections you want it to parse, if you pass an empty list then it only parses the default sections, which are prelude, input, molecule, rem, postlude and geometry.
<pre>
>> data = parser([])
>> for key in data.keys(): print(key)
prelude
input
molecule
rem
postlude
geometry
</pre>
However you can use the find_sections method to detect extra sections which may be parsed. In this example the output file is for a simple single-point calculation.
<pre>
>> print(parser.find_sections())
['input', 'sno', 'number_of_electrons', 'scf', 'mos']
>> data = parser(['number_of_electrons', 'scf'])
>> for key in data.keys(): print(key)
prelude
input
molecule
rem
number_of_electrons
scf
postlude
geometry
</pre>
Each of the keys corresponds to a dictionary containing the relevant information, for example we can look at the 'scf' information
<pre>
>> print(data['scf'])
{'cycles': {1: {'energy': -0.6434040867, 'diis error': 9.04e-17}, 2: {'energy': -1.0661086494, 'diis error': 9.04e-17}}, 'minima': {0: {}}}
</pre>

==[[RevQCMagic|Return]]==

Parsing a QChem Output File

2026-03-31T16:15:19Z

Jst55: /* Summary */

__TOC__

==Summary==
To extract all data from a QChem output file, you can use the QChemParser object from <pre>qcmagic.interfaces.parsers.qchem_parser.qchem_parser</pre>
Parsing is not automatic, you first have to create a parser object
<pre>parser = QChemParser('/path/to/file.out')</pre>
The actual parsing occurs when you call the parser object with a list of sections you want it to parse, if you pass an empty list then it only parses the default sections, which are prelude, input, molecule, rem, postlude and geometry.
<pre>
>> data = parser([])
>> for key in data.keys(): print(key)
prelude
input
molecule
rem
postlude
geometry
</pre>
However you can use the find_sections method to detect extra sections which may be parsed. In this example the output file is for a simple
<pre>
>> print(parser.find_sections())
['input', 'sno', 'number_of_electrons', 'scf', 'mos']
>> data = parser(['number_of_electrons', 'scf'])
>> for key in data.keys(): print(key)
prelude
input
molecule
rem
number_of_electrons
scf
postlude
geometry
</pre>
Each of the keys corresponds to a dictionary containing the relevant information, for example we can look at the 'scf' information
<pre>
>> print(data['scf'])
{'cycles': {1: {'energy': -0.6434040867, 'diis error': 9.04e-17}, 2: {'energy': -1.0661086494, 'diis error': 9.04e-17}}, 'minima': {0: {}}}
</pre>

==[[RevQCMagic|Return]]==

Parsing a QChem Output File

2026-03-31T14:56:52Z

Jst55:

__TOC__

==Summary==
To extract all data from a QChem output file, you can use the QChemParser object from <pre>qcmagic.interfaces.parsers.qchem_parser.qchem_parser</pre>

==[[RevQCMagic|Return]]==

Parsing a QChem Output File

2026-03-31T12:56:10Z

Jst55:

__TOC__

==Summary==

==[[RevQCMagic|Return]]==

Parsing a QChem Output File

2026-03-31T12:55:25Z

Jst55: Created page with "__TOC__ ==Summary=="

__TOC__

==Summary==

RevQCMagic

2026-03-31T12:54:22Z

Jst55: /* Quick Guides */

==Quick Guides==
[[Creating a QChem Input File]]

[[Parsing a QChem Output File]]

==Core Concepts==
[[Configurations and States]]

==[[Main Page#Computers#Software Tutorials|Return]]==

RevQCMagic

2026-03-31T12:54:12Z

Jst55: /* Quick Guides */

==Quick Guides==
[[Creating a QChem Input File]]
[[Parsing a QChem Output File]]

==Core Concepts==
[[Configurations and States]]

==[[Main Page#Computers#Software Tutorials|Return]]==

Configurations and States

2026-03-30T21:24:12Z

Jst55:

==Summary==
At the core of RevQCMagic are Configurations and States. Together these describe an entire system.

Take ground-state H2 with electronic configuration (1s)2, and ground-state HeH+ also with electronic configuration (1s)2. These two systems have different Configuration, but the same State.

Now consider ground-state H2 with electronic configuration (1s)2 and H2+ with electronic configuration (1s)1. These two systems have the same Configuration, but different State.

==Configuration==
A single Configuration object contains various SubConfigurations, such as geometry or basis set used etc. Configuration objects also keep track of the State objects they are associated with.

==SubConfiguration==

===Geometry===

===ConvolvedBasisSet===

==State==

==[[RevQCMagic|Return]]==

Configurations and States

2026-03-30T21:23:25Z

Jst55: /* SubConfiguration */

At the core of RevQCMagic are Configurations and States. Together these describe an entire system.

Take ground-state H2 with electronic configuration (1s)2, and ground-state HeH+ also with electronic configuration (1s)2. These two systems have different Configuration, but the same State.

Now consider ground-state H2 with electronic configuration (1s)2 and H2+ with electronic configuration (1s)1. These two systems have the same Configuration, but different State.

==Configuration==
A single Configuration object contains various SubConfigurations, such as geometry or basis set used etc. Configuration objects also keep track of the State objects they are associated with.

==SubConfiguration==

===Geometry===

===ConvolvedBasisSet===

==State==

==[[RevQCMagic|Return]]==

Configurations and States

2026-03-30T21:22:16Z

Jst55: /* Configuration */

Creating a QChem Input File

2026-03-30T21:08:00Z

Jst55: /* Building Configuration and QChemMetadata Manually */

__TOC__

==Summary==
RevQCMagic has an in-built QChem input file writer. The writer uses three things to generate an input file:
* Configuration (The Configuration object contains all information which gives a state context, i.e. it contains the nuclei involved, the geometry of the nuclei, the basis set for each atom, etc)
* MetaData (For a QChem input file this is a QChemMetadata object which contains all of the calculation parameters.)
* FilePath (The filepath to save the input file to.)

==Example: Building Configuration and QChemMetadata Manually==
<pre>
from qcmagic.core.cspace.configurationspace import Configuration
from qcmagic.core.cspace.molecule.atom import Atom
from qcmagic.core.cspace.molecule.atomfragment import AtomFragment
from qcmagic.core.cspace.molecule.geometry import Geometry
from qcmagic.auxiliary.linearalgebra3d import Vector3D
from qcmagic.auxiliary.qcmagic_standards import ANGSTROM_TO_BOHR

from qcmagic.interfaces.input_writers.qchem_input_writer.qchem_input_writer import (
QChemMetadata,
QChemInputWriter,
)

import numpy as np

def generate_H2_STO3G_Qchem_input_files():
# Each input file will have the same calculation parameters
parameters = {
'job_type': 'sp',
'basis': 'STO-3G',
'method': 'HF',
'symmetry_ignore': 'true',
'scf_convergence': '11',
'thresh': '14',
'unrestricted': 'false',
'iqmol_fchk': 'true',
'max_scf_cycles': '500',
'mem_total': '5976800'
}

# Create a QChemMetadata object to store the calculation parameters
# as well as the total charge (0) and the multiplicity (2*spin_proj+1)
metadata = QChemMetadata()
metadata.update_from_dictionary(parameters)
metadata.state_properties = {"total_charge": 0, "spin_projection": 0}

# Considering H-H bond lengths from 0.2 to 2,1 Angstroms
for radius in np.linspace(0.2, 2.1, 20):
# RevQCMagic uses Bohr whereas QChem uses Angstroms
radius_bohr = radius * ANGSTROM_TO_BOHR

# Every new geometry requires a new Configuration
config = Configuration()

# Generate a co-ordinate system for holding the molecule geometry
coordsystem = AtomFragment(parent=None)
H2 = AtomFragment(coordsystem)

# Add the two hydrogen atoms, note the required use of Vector3D
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, -radius_bohr/2])))
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, +radius_bohr/2])))

# Turn the AtomFragment object into a Geometry SubConfiguration, then
# add to the total Configuration
config.add_subconfiguration(Geometry([(None, None)], H2))

# Generate the input file writer using the Configuration, and use the
# QChemMetadata to write the specific input file to the specified filepath.
# If wanted to do different calculations on the same Configuration then could
# create different QChemMetadata objects and call the writer with each of them.
writer = QChemInputWriter(config)
filepath = f'H2_STO-3G_radius_{radius:.1f}A.inp'
writer(filepath, metadata)

generate_H2_STO3G_Qchem_input_files()
</pre>

The above code generates input files which all look like the one given below.

<pre>
$molecule
0 1
H +0.00000000000000 +0.00000000000000 -0.10000000000000
H +0.00000000000000 +0.00000000000000 +0.10000000000000
$end
$rem
basis STO-3G
job_type sp
method hf
symmetry_ignore true
scf_convergence 11
thresh 14
unrestricted false
iqmol_fchk true
max_scf_cycles 500
mem_total 5976800
$end
</pre>

==[[RevQCMagic|Return to RevQCMagic]]==

Creating a QChem Input File

2026-03-30T21:07:47Z

Jst55: /* Example: Generating QChem Input Files for Different H-H Bond Lengths */

__TOC__

==Summary==
RevQCMagic has an in-built QChem input file writer. The writer uses three things to generate an input file:
* Configuration (The Configuration object contains all information which gives a state context, i.e. it contains the nuclei involved, the geometry of the nuclei, the basis set for each atom, etc)
* MetaData (For a QChem input file this is a QChemMetadata object which contains all of the calculation parameters.)
* FilePath (The filepath to save the input file to.)

==Building Configuration and QChemMetadata Manually==
<pre>
from qcmagic.core.cspace.configurationspace import Configuration
from qcmagic.core.cspace.molecule.atom import Atom
from qcmagic.core.cspace.molecule.atomfragment import AtomFragment
from qcmagic.core.cspace.molecule.geometry import Geometry
from qcmagic.auxiliary.linearalgebra3d import Vector3D
from qcmagic.auxiliary.qcmagic_standards import ANGSTROM_TO_BOHR

from qcmagic.interfaces.input_writers.qchem_input_writer.qchem_input_writer import (
QChemMetadata,
QChemInputWriter,
)

import numpy as np

def generate_H2_STO3G_Qchem_input_files():
# Each input file will have the same calculation parameters
parameters = {
'job_type': 'sp',
'basis': 'STO-3G',
'method': 'HF',
'symmetry_ignore': 'true',
'scf_convergence': '11',
'thresh': '14',
'unrestricted': 'false',
'iqmol_fchk': 'true',
'max_scf_cycles': '500',
'mem_total': '5976800'
}

# Create a QChemMetadata object to store the calculation parameters
# as well as the total charge (0) and the multiplicity (2*spin_proj+1)
metadata = QChemMetadata()
metadata.update_from_dictionary(parameters)
metadata.state_properties = {"total_charge": 0, "spin_projection": 0}

# Considering H-H bond lengths from 0.2 to 2,1 Angstroms
for radius in np.linspace(0.2, 2.1, 20):
# RevQCMagic uses Bohr whereas QChem uses Angstroms
radius_bohr = radius * ANGSTROM_TO_BOHR

# Every new geometry requires a new Configuration
config = Configuration()

# Generate a co-ordinate system for holding the molecule geometry
coordsystem = AtomFragment(parent=None)
H2 = AtomFragment(coordsystem)

# Add the two hydrogen atoms, note the required use of Vector3D
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, -radius_bohr/2])))
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, +radius_bohr/2])))

# Turn the AtomFragment object into a Geometry SubConfiguration, then
# add to the total Configuration
config.add_subconfiguration(Geometry([(None, None)], H2))

# Generate the input file writer using the Configuration, and use the
# QChemMetadata to write the specific input file to the specified filepath.
# If wanted to do different calculations on the same Configuration then could
# create different QChemMetadata objects and call the writer with each of them.
writer = QChemInputWriter(config)
filepath = f'H2_STO-3G_radius_{radius:.1f}A.inp'
writer(filepath, metadata)

generate_H2_STO3G_Qchem_input_files()
</pre>

The above code generates input files which all look like the one given below.

<pre>
$molecule
0 1
H +0.00000000000000 +0.00000000000000 -0.10000000000000
H +0.00000000000000 +0.00000000000000 +0.10000000000000
$end
$rem
basis STO-3G
job_type sp
method hf
symmetry_ignore true
scf_convergence 11
thresh 14
unrestricted false
iqmol_fchk true
max_scf_cycles 500
mem_total 5976800
$end
</pre>

==[[RevQCMagic|Return to RevQCMagic]]==

Creating a QChem Input File

2026-03-30T21:06:16Z

Jst55:

__TOC__

==Summary==
RevQCMagic has an in-built QChem input file writer. The writer uses three things to generate an input file:
* Configuration (The Configuration object contains all information which gives a state context, i.e. it contains the nuclei involved, the geometry of the nuclei, the basis set for each atom, etc)
* MetaData (For a QChem input file this is a QChemMetadata object which contains all of the calculation parameters.)
* FilePath (The filepath to save the input file to.)

==Example: Generating QChem Input Files for Different H-H Bond Lengths==
<pre>
from qcmagic.core.cspace.configurationspace import Configuration
from qcmagic.core.cspace.molecule.atom import Atom
from qcmagic.core.cspace.molecule.atomfragment import AtomFragment
from qcmagic.core.cspace.molecule.geometry import Geometry
from qcmagic.auxiliary.linearalgebra3d import Vector3D
from qcmagic.auxiliary.qcmagic_standards import ANGSTROM_TO_BOHR

from qcmagic.interfaces.input_writers.qchem_input_writer.qchem_input_writer import (
QChemMetadata,
QChemInputWriter,
)

import numpy as np

def generate_H2_STO3G_Qchem_input_files():
# Each input file will have the same calculation parameters
parameters = {
'job_type': 'sp',
'basis': 'STO-3G',
'method': 'HF',
'symmetry_ignore': 'true',
'scf_convergence': '11',
'thresh': '14',
'unrestricted': 'false',
'iqmol_fchk': 'true',
'max_scf_cycles': '500',
'mem_total': '5976800'
}

# Create a QChemMetadata object to store the calculation parameters
# as well as the total charge (0) and the multiplicity (2*spin_proj+1)
metadata = QChemMetadata()
metadata.update_from_dictionary(parameters)
metadata.state_properties = {"total_charge": 0, "spin_projection": 0}

# Considering H-H bond lengths from 0.2 to 2,1 Angstroms
for radius in np.linspace(0.2, 2.1, 20):
# RevQCMagic uses Bohr whereas QChem uses Angstroms
radius_bohr = radius * ANGSTROM_TO_BOHR

# Every new geometry requires a new Configuration
config = Configuration()

# Generate a co-ordinate system for holding the molecule geometry
coordsystem = AtomFragment(parent=None)
H2 = AtomFragment(coordsystem)

# Add the two hydrogen atoms, note the required use of Vector3D
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, -radius_bohr/2])))
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, +radius_bohr/2])))

# Turn the AtomFragment object into a Geometry SubConfiguration, then
# add to the total Configuration
config.add_subconfiguration(Geometry([(None, None)], H2))

# Generate the input file writer using the Configuration, and use the
# QChemMetadata to write the specific input file to the specified filepath.
# If wanted to do different calculations on the same Configuration then could
# create different QChemMetadata objects and call the writer with each of them.
writer = QChemInputWriter(config)
filepath = f'H2_STO-3G_radius_{radius:.1f}A.inp'
writer(filepath, metadata)

generate_H2_STO3G_Qchem_input_files()
</pre>

The above code generates input files which all look like the one given below.

<pre>
$molecule
0 1
H +0.00000000000000 +0.00000000000000 -0.10000000000000
H +0.00000000000000 +0.00000000000000 +0.10000000000000
$end
$rem
basis STO-3G
job_type sp
method hf
symmetry_ignore true
scf_convergence 11
thresh 14
unrestricted false
iqmol_fchk true
max_scf_cycles 500
mem_total 5976800
$end
</pre>

==[[RevQCMagic|Return to RevQCMagic]]==

Configurations and States

2026-03-30T21:02:37Z

Jst55:

Configurations and States

2026-03-30T21:01:55Z

Jst55: Created page with "At the core of RevQCMagic are Configurations and States. Together these describe an entire system. Take ground-state H2 with electronic configuration (1s)2, and ground-state HeH+ also with electronic configuration (1s)2. These two systems have different Configuration, but the same State. Now consider ground-state H2 with electronic configuration (1s)2 and H2+ with electronic configu..."

Creating a QChem Input File

2026-03-30T20:19:30Z

Jst55:

RevQCMagic has an in-built QChem input file writer. The writer uses three things to generate an input file:
* Configuration (The Configuration object contains all information which gives a state context, i.e. it contains the nuclei involved, the geometry of the nuclei, the basis set for each atom, etc)
* MetaData (For a QChem input file this is a QChemMetadata object which contains all of the calculation parameters.)
* FilePath (The filepath to save the input file to.)

==Example: Generating QChem Input Files for Different H-H Bond Lengths==
<pre>
from qcmagic.core.cspace.configurationspace import Configuration
from qcmagic.core.cspace.molecule.atom import Atom
from qcmagic.core.cspace.molecule.atomfragment import AtomFragment
from qcmagic.core.cspace.molecule.geometry import Geometry
from qcmagic.auxiliary.linearalgebra3d import Vector3D
from qcmagic.auxiliary.qcmagic_standards import ANGSTROM_TO_BOHR

from qcmagic.interfaces.input_writers.qchem_input_writer.qchem_input_writer import (
QChemMetadata,
QChemInputWriter,
)

import numpy as np

def generate_H2_STO3G_Qchem_input_files():
# Each input file will have the same calculation parameters
parameters = {
'job_type': 'sp',
'basis': 'STO-3G',
'method': 'HF',
'symmetry_ignore': 'true',
'scf_convergence': '11',
'thresh': '14',
'unrestricted': 'false',
'iqmol_fchk': 'true',
'max_scf_cycles': '500',
'mem_total': '5976800'
}

# Create a QChemMetadata object to store the calculation parameters
# as well as the total charge (0) and the multiplicity (2*spin_proj+1)
metadata = QChemMetadata()
metadata.update_from_dictionary(parameters)
metadata.state_properties = {"total_charge": 0, "spin_projection": 0}

# Considering H-H bond lengths from 0.2 to 2,1 Angstroms
for radius in np.linspace(0.2, 2.1, 20):
# RevQCMagic uses Bohr whereas QChem uses Angstroms
radius_bohr = radius * ANGSTROM_TO_BOHR

# Every new geometry requires a new Configuration
config = Configuration()

# Generate a co-ordinate system for holding the molecule geometry
coordsystem = AtomFragment(parent=None)
H2 = AtomFragment(coordsystem)

# Add the two hydrogen atoms, note the required use of Vector3D
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, -radius_bohr/2])))
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, +radius_bohr/2])))

# Turn the AtomFragment object into a Geometry SubConfiguration, then
# add to the total Configuration
config.add_subconfiguration(Geometry([(None, None)], H2))

# Generate the input file writer using the Configuration, and use the
# QChemMetadata to write the specific input file to the specified filepath.
# If wanted to do different calculations on the same Configuration then could
# create different QChemMetadata objects and call the writer with each of them.
writer = QChemInputWriter(config)
filepath = f'H2_STO-3G_radius_{radius:.1f}A.inp'
writer(filepath, metadata)

generate_H2_STO3G_Qchem_input_files()
</pre>

The above code generates input files which all look like the one given below.

<pre>
$molecule
0 1
H +0.00000000000000 +0.00000000000000 -0.10000000000000
H +0.00000000000000 +0.00000000000000 +0.10000000000000
$end
$rem
basis STO-3G
job_type sp
method hf
symmetry_ignore true
scf_convergence 11
thresh 14
unrestricted false
iqmol_fchk true
max_scf_cycles 500
mem_total 5976800
$end
</pre>

==[[RevQCMagic|Return to RevQCMagic]]==

Creating a QChem Input File

2026-03-30T20:13:46Z

Jst55:

RevQCMagic has an in-built QChem input file writer. The writer uses four things to generate an input file:
* Configuration (The Configuration object contains all information which gives a state context, i.e. it contains the nuclei involved, the geometry of the nuclei, the basis set for each atom, etc)
* MetaData (For a QChem input file this is the total charge and the spin.)
* Parameters (These are all of the calculation details such as DFT functional, SCF convergence criteria, etc.)
* FilePath (The filepath to save the input file to.)

==Example: Generating QChem Input Files for Different H-H Bond Lengths==
<pre>
from qcmagic.core.cspace.configurationspace import Configuration
from qcmagic.core.cspace.molecule.atom import Atom
from qcmagic.core.cspace.molecule.atomfragment import AtomFragment
from qcmagic.core.cspace.molecule.geometry import Geometry
from qcmagic.auxiliary.linearalgebra3d import Vector3D
from qcmagic.auxiliary.qcmagic_standards import ANGSTROM_TO_BOHR

from qcmagic.interfaces.input_writers.qchem_input_writer.qchem_input_writer import (
QChemMetadata,
QChemInputWriter,
)

import numpy as np

def generate_H2_STO3G_Qchem_input_files():
# Each input file will have the same calculation parameters
parameters = {
'job_type': 'sp',
'basis': 'STO-3G',
'method': 'HF',
'symmetry_ignore': 'true',
'scf_convergence': '11',
'thresh': '14',
'unrestricted': 'false',
'iqmol_fchk': 'true',
'max_scf_cycles': '500',
'mem_total': '5976800'
}

# Create a QChemMetadata object to store the calculation parameters
# as well as the total charge (0) and the multiplicity (2*spin_proj+1)
metadata = QChemMetadata()
metadata.update_from_dictionary(parameters)
metadata.state_properties = {"total_charge": 0, "spin_projection": 0}

# Considering H-H bond lengths from 0.2 to 2,1 Angstroms
for radius in np.linspace(0.2, 2.1, 20):
# RevQCMagic uses Bohr whereas QChem uses Angstroms
radius_bohr = radius * ANGSTROM_TO_BOHR

# Every new geometry requires a new Configuration
config = Configuration()

# Generate a co-ordinate system for holding the molecule geometry
coordsystem = AtomFragment(parent=None)
H2 = AtomFragment(coordsystem)

# Add the two hydrogen atoms, note the required use of Vector3D
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, -radius_bohr/2])))
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, +radius_bohr/2])))

# Turn the AtomFragment object into a Geometry SubConfiguration, then
# add to the total Configuration
config.add_subconfiguration(Geometry([(None, None)], H2))

# Generate the input file writer using the Configuration, and use the
# QChemMetadata to write the specific input file to the specified filepath.
# If wanted to do different calculations on the same Configuration then could
# create different QChemMetadata objects and call the writer with each of them.
writer = QChemInputWriter(config)
filepath = f'H2_STO-3G_radius_{radius:.1f}A.inp'
writer(filepath, metadata)

generate_H2_STO3G_Qchem_input_files()
</pre>

The above code generates input files which all look like the one given below.

<pre>
$molecule
0 1
H +0.00000000000000 +0.00000000000000 -0.10000000000000
H +0.00000000000000 +0.00000000000000 +0.10000000000000
$end
$rem
basis STO-3G
job_type sp
method hf
symmetry_ignore true
scf_convergence 11
thresh 14
unrestricted false
iqmol_fchk true
max_scf_cycles 500
mem_total 5976800
$end
</pre>

==[[RevQCMagic|Return to RevQCMagic]]==

Creating a QChem Input File

2026-03-30T18:34:28Z

Jst55:

RevQCMagic has an in-built QChem input file writer. The writer uses four things to generate an input file:
* Configuration (The Configuration object contains all information which gives a state context, i.e. it contains the nuclei involved, the geometry of the nuclei, the basis set for each atom, etc)
* MetaData (For a QChem input file this is the total charge and the spin.)
* Parameters (These are all of the calculation details such as DFT functional, SCF convergence criteria, etc.)
* FilePath (The filepath to save the input file to.)

==Example: Generating QChem Input Files for Different H-H Bond Lengths==
<pre>
from qcmagic.core.cspace.configurationspace import Configuration
from qcmagic.core.cspace.molecule.atom import Atom
from qcmagic.core.cspace.molecule.atomfragment import AtomFragment
from qcmagic.core.cspace.molecule.geometry import Geometry
from qcmagic.auxiliary.linearalgebra3d import Vector3D
from qcmagic.auxiliary.qcmagic_standards import ANGSTROM_TO_BOHR

from qcmagic.interfaces.input_writers.qchem_input_writer.qchem_input_writer import (
QChemMetadata,
QChemInputWriter,
)

import numpy as np

def generate_H2_STO3G_Qchem_input_files():
# Considering H-H bond lengths from 0.2 to 2,1 Angstroms
for radius in np.linspace(0.2, 2.1, 20):
# RevQCMagic uses Bohr whereas QChem uses Angstroms
radius_bohr = radius * ANGSTROM_TO_BOHR

# For each new bond length define a new configuration
config = Configuration()
metadata = QChemMetadata()

parameters = {
'job_type': 'sp',
'basis': 'STO-3G',
'method': 'HF',
'symmetry_ignore': 'true',
'scf_convergence': '11',
'thresh': '14',
'unrestricted': 'false',
'iqmol_fchk': 'true',
'max_scf_cycles': '500',
'mem_total': '5976800'
}
metadata.update_from_dictionary(parameters)
metadata.state_properties = {"total_charge": 0, "spin_projection": 0}

coordsystem = AtomFragment(parent=None)
H2 = AtomFragment(coordsystem)

H2.add(Atom('H', H2, Vector3D([0.00, 0.00, -radius_bohr/2])))
H2.add(Atom('H', H2, Vector3D([0.00, 0.00, +radius_bohr/2])))

config.add_subconfiguration(Geometry([(None, None)], H2))

writer = QChemInputWriter(config)
filepath = f'H2_STO-3G_radius_{radius:.1f}A.inp'
writer(filepath, metadata)

generate_H2_STO3G_Qchem_input_files()
</pre>

The above code generates input files which all look like the one given below.

<pre>
$molecule
0 1
H +0.00000000000000 +0.00000000000000 -0.10000000000000
H +0.00000000000000 +0.00000000000000 +0.10000000000000
$end
$rem
basis STO-3G
job_type sp
method hf
symmetry_ignore true
scf_convergence 11
thresh 14
unrestricted false
iqmol_fchk true
max_scf_cycles 500
mem_total 5976800
$end
</pre>

==[[RevQCMagic|Return to RevQCMagic]]==

Creating a QChem Input File

2026-03-30T18:13:37Z

Jst55:

RevQCMagic

2026-03-30T18:10:49Z

Jst55: /* Return to Main Page */

==Quick Guides==
[[Creating a QChem Input File]]

==Core Concepts==
[[Configurations and States]]

==[[Main Page#Computers#Software Tutorials|Return]]==

Creating a QChem Input File

2026-03-30T18:08:58Z

Jst55:

RevQCMagic

2026-03-30T18:07:06Z

Jst55:

==Quick Guides==
[[Creating a QChem Input File]]

==Core Concepts==
[[Configurations and States]]

==Return to Main Page==
[[Main Page]]

Creating a QChem Input File

2026-03-30T17:10:55Z

Jst55: /* Creating a QChem Input File */

Creating a QChem Input File

2026-03-30T17:03:52Z

Jst55: Created page with "==Creating a QChem Input File=="

==Creating a QChem Input File==

RevQCMagic

2026-03-30T17:02:59Z

Jst55: Created page with "==Quick Guides== Creating a QChem Input File ==Core Concepts== Configurations and States"

==Quick Guides==
[[Creating a QChem Input File]]

==Core Concepts==
[[Configurations and States]]

Main Page

2026-03-30T17:01:15Z

Jst55: /* Software Tutorials */

<div style="display:flex; flex-wrap:wrap; justify-content:center; gap:1em; align-items:flex-start; margin:1em 0;">

<div style="overflow-x:auto; max-width:100%;">
<pre style="display:inline-block; text-align:left; white-space:pre; margin:0; padding:1em 1.5em; border:2px solid #7c3aed; border-radius:12px; background:#0f172a; box-shadow:0 0 12px rgba(124,58,237,0.45);">
 _________ ___ ___ ______ ___ __ __ 
/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ 
\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ 
 \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ 
 \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ 
 \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ 
 \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ 
</pre>
</div>

<div style="overflow-x:auto; max-width:100%;">
<pre style="display:inline-block; text-align:left; white-space:pre; margin:0; padding:1em 1.5em; border:2px solid #7c3aed; border-radius:12px; background:#0f172a; box-shadow:0 0 12px rgba(124,58,237,0.45);">
 _______ ______ ______ __ __ ______ 
/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ 
\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ 
 \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ 
 \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ 
 \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ 
 \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ 
</pre>
</div>

</div>

=About=

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki (apparently evenings are good times to read the Wiki). In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos. For members of the group please feel free to edit the contents of the wiki and fix any errors that you are bound to spot.

== [[Group_List | Group List and Photos]] ==

Here you can find photos of the group in various locations. There is also a helpful Gantt chart illustrating the storied group history. The chart should ideally be updated termly, the current chart maintainer is Luke Wright and you should email him with any complaints.

== [[Summer_Interns | Summer Interns]] ==

Email theory-sec@ch.cam.ac.uk for summer internship opportunities in the group. You are welcome to suggest ideas for a project you would like to do, but ideas are also available for assignment.

==[https://www.overleaf.com/read/yddfjrvpjckj Group Expectations]==

The Group Expectations document is available on Overleaf above. The rules outlined must be obeyed at all costs, if not, the consequences are dire.

=Events=

This section contains information and dates about all regularly or spontaneously scheduled academic events.

==[https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745 Group Calendar]==
The group calendar is available at the link above. For maximum group efficiency you should add this calendar to your personal calendar. Instructions for how to do this are pending if I can be bothered to write them.

{{Special:IframePage}}

==[[Past Group Meetings|Group Meetings]]==

Group Meetings take place every Thursday at 15.30 in U203. For anyone who needs to book a room for group meetings (or otherwise), follow this link [https://bookings.ch.cam.ac.uk/lecture-theatres/mrbs/ here] to see room availability. The current term's group meetings are available below, so that you need not click the above link (which contains past group meetings).

===Easter 2026===
{| class="wikitable"
! style="width: 20ex;" | Date
! style="width: 18ex;" | Talk
! style="width: 18ex;" | Cake
|-
| 30 April || Luke + Corey + Katrina || Luke
|-
| 7 May || Informal ||
|-
| 14 May || Reka ||
|-
| 21 May || Informal ||
|-
| 28 May || MPhil ||
|-
| 4 June || Informal ||
|-
| 11 June || Dylan ||
|-
| 18 June || Informal ||
|}

==Journal Club==
Journal Club occurs about twice a term, it usually occurs at 12pm in one of the Cybercafe rooms (U202 or U203) pizza or alternatives are provided. Upcoming and Past Journal Clubs are found [[Journal Clubs|here]].

==Seminars==

* [https://www.lclu.cam.ac.uk/events/coffee-meetings Leverhulme Centre for Life in the Universe Coffee Meetings]
* [https://lists.cam.ac.uk/sympa/subscribe/phy-cavendish-quantum-info?previous_action=info Quantum Information Seminars]

==QCQCDG==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available [https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group here].

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Wednesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

= Research and Projects =

== [[Project_Ideas | Project Ideas]] ==
Based on recent talks and conferences. Contains both project ideas and more general questions that would be nice to answer.

== Dissertations ==
Please upload any missing documents to these folders such that these contain a complete history of every project or work completed in the group.
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]
* [https://www.overleaf.com/read/ffdvzskxvnbm#2e9673 Template for LATEX poster]

== Quantum computing Open Questions ==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

= Computers =

This section contains all information you could ever need about computers and how to use them.

== [[Computer_and_Storage_List | Computing Resources]] ==

See this section for what computers the group members are using, what compute clusters are available, and where you can store files.

== [[Introduction | Introduction to basic shell commands]] ==
There are a number of tutorials available which document basic operations that are useful. Some highlights include setting up SSH keys, X-forwarding, or how to use vim. Click the hyperlink for the full list.

== [[Connecting_Machines | How to connect to department machines]] ==

It can be useful often to connect to computers in department remotely. Please keep your work-life balance in mind.

== [[Installing_Slack | How to install Slack on department machines ]] ==

Group communication is done primarily through Slack, it may be useful to install it. Alternatively we could begin using pigeon-mail or smoke signals.

== Software Tutorials==
# [[QChem]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]
# [[RevQCMagic]]

= Uncategorisable =

The following sections could not be given a heading in the great wiki organisation of 2026 and thus are labelled as uncategorisable. See [https://en.wikipedia.org/wiki/Russell%27s_paradox Russell's paradox] for more details.

== Useful Information ==

Here are some things that were deemed as useful once upon a time. Please add to the list.

# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# Where to get [[Travel Money]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

== [[Archiving_data | Archiving data for the university repository]] ==

For publications data must be archived in accordance with university policy, instructions are here.

== [[Website_to_do | To-do list for the Thom Group Website]] ==

If there are desired wiki changes but the will to implement is not there they can be written here.

= Archive =

Anything not updated for more than 5 years should be put into this section.

== [[Group_activities | Group Activities]] ==

Main Page

2026-03-30T17:01:07Z

Jst55: /* Software Tutorials */

<div style="display:flex; flex-wrap:wrap; justify-content:center; gap:1em; align-items:flex-start; margin:1em 0;">

<div style="overflow-x:auto; max-width:100%;">
<pre style="display:inline-block; text-align:left; white-space:pre; margin:0; padding:1em 1.5em; border:2px solid #7c3aed; border-radius:12px; background:#0f172a; box-shadow:0 0 12px rgba(124,58,237,0.45);">
 _________ ___ ___ ______ ___ __ __ 
/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ 
\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ 
 \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ 
 \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ 
 \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ 
 \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ 
</pre>
</div>

<div style="overflow-x:auto; max-width:100%;">
<pre style="display:inline-block; text-align:left; white-space:pre; margin:0; padding:1em 1.5em; border:2px solid #7c3aed; border-radius:12px; background:#0f172a; box-shadow:0 0 12px rgba(124,58,237,0.45);">
 _______ ______ ______ __ __ ______ 
/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ 
\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ 
 \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ 
 \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ 
 \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ 
 \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ 
</pre>
</div>

</div>

=About=

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki (apparently evenings are good times to read the Wiki). In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos. For members of the group please feel free to edit the contents of the wiki and fix any errors that you are bound to spot.

== [[Group_List | Group List and Photos]] ==

Here you can find photos of the group in various locations. There is also a helpful Gantt chart illustrating the storied group history. The chart should ideally be updated termly, the current chart maintainer is Luke Wright and you should email him with any complaints.

== [[Summer_Interns | Summer Interns]] ==

Email theory-sec@ch.cam.ac.uk for summer internship opportunities in the group. You are welcome to suggest ideas for a project you would like to do, but ideas are also available for assignment.

==[https://www.overleaf.com/read/yddfjrvpjckj Group Expectations]==

The Group Expectations document is available on Overleaf above. The rules outlined must be obeyed at all costs, if not, the consequences are dire.

=Events=

This section contains information and dates about all regularly or spontaneously scheduled academic events.

==[https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745 Group Calendar]==
The group calendar is available at the link above. For maximum group efficiency you should add this calendar to your personal calendar. Instructions for how to do this are pending if I can be bothered to write them.

{{Special:IframePage}}

==[[Past Group Meetings|Group Meetings]]==

Group Meetings take place every Thursday at 15.30 in U203. For anyone who needs to book a room for group meetings (or otherwise), follow this link [https://bookings.ch.cam.ac.uk/lecture-theatres/mrbs/ here] to see room availability. The current term's group meetings are available below, so that you need not click the above link (which contains past group meetings).

===Easter 2026===
{| class="wikitable"
! style="width: 20ex;" | Date
! style="width: 18ex;" | Talk
! style="width: 18ex;" | Cake
|-
| 30 April || Luke + Corey + Katrina || Luke
|-
| 7 May || Informal ||
|-
| 14 May || Reka ||
|-
| 21 May || Informal ||
|-
| 28 May || MPhil ||
|-
| 4 June || Informal ||
|-
| 11 June || Dylan ||
|-
| 18 June || Informal ||
|}

==Journal Club==
Journal Club occurs about twice a term, it usually occurs at 12pm in one of the Cybercafe rooms (U202 or U203) pizza or alternatives are provided. Upcoming and Past Journal Clubs are found [[Journal Clubs|here]].

==Seminars==

* [https://www.lclu.cam.ac.uk/events/coffee-meetings Leverhulme Centre for Life in the Universe Coffee Meetings]
* [https://lists.cam.ac.uk/sympa/subscribe/phy-cavendish-quantum-info?previous_action=info Quantum Information Seminars]

==QCQCDG==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available [https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group here].

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Wednesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

= Research and Projects =

== [[Project_Ideas | Project Ideas]] ==
Based on recent talks and conferences. Contains both project ideas and more general questions that would be nice to answer.

== Dissertations ==
Please upload any missing documents to these folders such that these contain a complete history of every project or work completed in the group.
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]
* [https://www.overleaf.com/read/ffdvzskxvnbm#2e9673 Template for LATEX poster]

== Quantum computing Open Questions ==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

= Computers =

This section contains all information you could ever need about computers and how to use them.

== [[Computer_and_Storage_List | Computing Resources]] ==

See this section for what computers the group members are using, what compute clusters are available, and where you can store files.

== [[Introduction | Introduction to basic shell commands]] ==
There are a number of tutorials available which document basic operations that are useful. Some highlights include setting up SSH keys, X-forwarding, or how to use vim. Click the hyperlink for the full list.

== [[Connecting_Machines | How to connect to department machines]] ==

It can be useful often to connect to computers in department remotely. Please keep your work-life balance in mind.

== [[Installing_Slack | How to install Slack on department machines ]] ==

Group communication is done primarily through Slack, it may be useful to install it. Alternatively we could begin using pigeon-mail or smoke signals.

== Software Tutorials==
# [[QChem]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]
# [[RevQCMagic

= Uncategorisable =

The following sections could not be given a heading in the great wiki organisation of 2026 and thus are labelled as uncategorisable. See [https://en.wikipedia.org/wiki/Russell%27s_paradox Russell's paradox] for more details.

== Useful Information ==

Here are some things that were deemed as useful once upon a time. Please add to the list.

# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# Where to get [[Travel Money]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

== [[Archiving_data | Archiving data for the university repository]] ==

For publications data must be archived in accordance with university policy, instructions are here.

== [[Website_to_do | To-do list for the Thom Group Website]] ==

If there are desired wiki changes but the will to implement is not there they can be written here.

= Archive =

Anything not updated for more than 5 years should be put into this section.

== [[Group_activities | Group Activities]] ==