From 54ec28466373aa7a2413b89a8aae01b446cc762e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 22 Mar 2024 13:07:14 +0000 Subject: [PATCH] chore(docs): render docs --- _reference/utils.qmd | 18 +++--- docs/_reference/utils.html | 10 +-- docs/guide/explanation/index.html | 2 +- docs/guide/how-to/index.html | 10 +-- docs/guide/tutorials/getting-started.html | 2 +- docs/guide/tutorials/index.html | 6 +- docs/search.json | 4 +- docs/sitemap.xml | 76 +++++++++++------------ 8 files changed, 64 insertions(+), 64 deletions(-) diff --git a/_reference/utils.qmd b/_reference/utils.qmd index bb53bd92..aec31bc6 100644 --- a/_reference/utils.qmd +++ b/_reference/utils.qmd @@ -95,7 +95,7 @@ Run command in shell and capture stdout. ### morse_transition_rate { #kimmdy.utils.morse_transition_rate } -`utils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)` +`utils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)` Calculates reaction rate constant for a bond breaking event. @@ -108,14 +108,14 @@ The calculation should be according to the derivation in the original KIMMDY pap #### Parameters -| Name | Type | Description | Default | -|----------------|------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------| -| `r_curr` | [list](`list`)\[[float](`float`)\] | Bond distances for a single bond, typically from a time series. | _required_ | -| `r_0` | [float](`float`) | Equilibrium bond length of the bond. | _required_ | -| `dissociation` | | Dissociation energy of the bond. | _required_ | -| `k_f` | [float](`float`) | Spring constant of the bond. | _required_ | -| `k_0` | [float](`float`) | Prefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m). | `0.288` | -| `kT` | [float](`float`) | Constant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K. | `2.479` | +| Name | Type | Description | Default | +|--------------------|------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------| +| `r_curr` | [list](`list`)\[[float](`float`)\] | Bond distances for a single bond, typically from a time series. | _required_ | +| `r_0` | [float](`float`) | Equilibrium bond length of the bond. | _required_ | +| `dissociation` | | Dissociation energy of the bond. | _required_ | +| `k_f` | [float](`float`) | Spring constant of the bond. | _required_ | +| `frequency_factor` | [float](`float`) | Prefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m). | `0.288` | +| `temperature` | [float](`float`) | Temperature for the Arrhenius equation in GROMACS units. | `300` | ### run_gmx { #kimmdy.utils.run_gmx } diff --git a/docs/_reference/utils.html b/docs/_reference/utils.html index 23f9d7ff..32c1890c 100644 --- a/docs/_reference/utils.html +++ b/docs/_reference/utils.html @@ -692,7 +692,7 @@

get_shell_st

morse_transition_rate

-

utils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)

+

utils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)

Calculates reaction rate constant for a bond breaking event.

Uses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.

The calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786

@@ -733,16 +733,16 @@

Parameters

required -k_0 +frequency_factor float Prefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m). 0.288 -kT +temperature float -Constant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K. -2.479 +Temperature for the Arrhenius equation in GROMACS units. +300 diff --git a/docs/guide/explanation/index.html b/docs/guide/explanation/index.html index ac315aaf..985c492f 100644 --- a/docs/guide/explanation/index.html +++ b/docs/guide/explanation/index.html @@ -537,7 +537,7 @@

Explanations

- + Visualize Topologies diff --git a/docs/guide/how-to/index.html b/docs/guide/how-to/index.html index 01e3ec28..58970d27 100644 --- a/docs/guide/how-to/index.html +++ b/docs/guide/how-to/index.html @@ -537,7 +537,7 @@

How-To

- + Contribute @@ -545,7 +545,7 @@

How-To

  - + Examples @@ -553,7 +553,7 @@

How-To

  - + High Performance Computing @@ -561,7 +561,7 @@

How-To

  - + Install Machine Learning Plugins @@ -569,7 +569,7 @@

How-To

  - + Reaction only diff --git a/docs/guide/tutorials/getting-started.html b/docs/guide/tutorials/getting-started.html index 2541aaa5..adc35253 100644 --- a/docs/guide/tutorials/getting-started.html +++ b/docs/guide/tutorials/getting-started.html @@ -603,7 +603,7 @@

Setup the Simulation<

Our starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin hat_reaction to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.

diff --git a/docs/guide/tutorials/index.html b/docs/guide/tutorials/index.html index ca6d5070..05ed5803 100644 --- a/docs/guide/tutorials/index.html +++ b/docs/guide/tutorials/index.html @@ -507,7 +507,7 @@

Tutorials

-
+

@@ -539,7 +539,7 @@

-
+

@@ -571,7 +571,7 @@

-
+

 

diff --git a/docs/search.json b/docs/search.json index da245a23..8bbdeb44 100644 --- a/docs/search.json +++ b/docs/search.json @@ -466,7 +466,7 @@ "href": "_reference/utils.html", "title": "utils", "section": "", - "text": "utils\nUtilities for building plugins, shell convenience functions and GROMACS related functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyAtomAddress\nAddress to an atom in the topology.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nk_0\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\nkT\nfloat\nConstant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K.\n2.479\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired" + "text": "utils\nUtilities for building plugins, shell convenience functions and GROMACS related functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyAtomAddress\nAddress to an atom in the topology.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nfrequency_factor\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\ntemperature\nfloat\nTemperature for the Arrhenius equation in GROMACS units.\n300\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired" }, { "objectID": "_reference/utils.html#attributes", @@ -480,7 +480,7 @@ "href": "_reference/utils.html#functions", "title": "utils", "section": "", - "text": "Name\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nk_0\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\nkT\nfloat\nConstant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K.\n2.479\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired" + "text": "Name\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nfrequency_factor\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\ntemperature\nfloat\nTemperature for the Arrhenius equation in GROMACS units.\n300\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired" }, { "objectID": "_reference/cmd.html", diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 3644b950..275eff9c 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -2,154 +2,154 @@ http://hits-mbm-dev.github.io/kimmdy/guide/explanation/index.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/guide/how-to/index.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/guide/how-to/examples.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/guide/how-to/hcp.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/guide/references/input.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/getting-started.html - 2024-03-19T10:42:20.650Z + 2024-03-22T13:05:41.432Z http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/colbuilder.html - 2024-03-19T10:42:20.650Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.TopologyDict.html - 2024-03-19T10:43:19.918Z + 2024-03-22T13:06:35.916Z http://hits-mbm-dev.github.io/kimmdy/_reference/topology.ff.html - 2024-03-19T10:43:19.826Z + 2024-03-22T13:06:35.824Z http://hits-mbm-dev.github.io/kimmdy/_reference/index.html - 2024-03-19T10:43:19.774Z + 2024-03-22T13:06:35.768Z http://hits-mbm-dev.github.io/kimmdy/_reference/config.html - 2024-03-19T10:43:19.974Z + 2024-03-22T13:06:35.972Z http://hits-mbm-dev.github.io/kimmdy/_reference/kmc.html - 2024-03-19T10:43:20.018Z + 2024-03-22T13:06:36.012Z http://hits-mbm-dev.github.io/kimmdy/_reference/topology.topology.html - 2024-03-19T10:43:19.826Z + 2024-03-22T13:06:35.820Z http://hits-mbm-dev.github.io/kimmdy/_reference/schema.html - 2024-03-19T10:43:20.130Z + 2024-03-22T13:06:36.124Z http://hits-mbm-dev.github.io/kimmdy/_reference/homolysis.reaction.Homolysis.html - 2024-03-19T10:43:20.194Z + 2024-03-22T13:06:36.192Z http://hits-mbm-dev.github.io/kimmdy/_reference/recipe.html - 2024-03-19T10:43:20.102Z + 2024-03-22T13:06:36.096Z http://hits-mbm-dev.github.io/kimmdy/_reference/analysis.html - 2024-03-19T10:43:19.954Z + 2024-03-22T13:06:35.948Z http://hits-mbm-dev.github.io/kimmdy/_reference/hat_naive.reaction.NaiveHAT.html - 2024-03-19T10:43:20.198Z + 2024-03-22T13:06:36.196Z http://hits-mbm-dev.github.io/kimmdy/_reference/topology.atomic.html - 2024-03-19T10:43:19.918Z + 2024-03-22T13:06:35.912Z http://hits-mbm-dev.github.io/kimmdy/index.html - 2024-03-19T10:42:20.654Z + 2024-03-22T13:05:41.436Z http://hits-mbm-dev.github.io/kimmdy/_reference/dummyreaction.reaction.DummyReaction.html - 2024-03-19T10:43:20.198Z + 2024-03-22T13:06:36.196Z http://hits-mbm-dev.github.io/kimmdy/_reference/constants.html - 2024-03-19T10:43:19.978Z + 2024-03-22T13:06:35.972Z http://hits-mbm-dev.github.io/kimmdy/_reference/tasks.html - 2024-03-19T10:43:20.142Z + 2024-03-22T13:06:36.140Z http://hits-mbm-dev.github.io/kimmdy/_reference/plugins.html - 2024-03-19T10:43:20.054Z + 2024-03-22T13:06:36.052Z http://hits-mbm-dev.github.io/kimmdy/_reference/tools.html - 2024-03-19T10:43:20.166Z + 2024-03-22T13:06:36.164Z http://hits-mbm-dev.github.io/kimmdy/_reference/coordinates.html - 2024-03-19T10:43:19.998Z + 2024-03-22T13:06:35.992Z http://hits-mbm-dev.github.io/kimmdy/_reference/utils.html - 2024-03-19T10:43:20.194Z + 2024-03-22T13:06:36.192Z http://hits-mbm-dev.github.io/kimmdy/_reference/cmd.html - 2024-03-19T10:43:19.798Z + 2024-03-22T13:06:35.792Z http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.html - 2024-03-19T10:43:20.046Z + 2024-03-22T13:06:36.040Z http://hits-mbm-dev.github.io/kimmdy/_reference/runmanager.html - 2024-03-19T10:43:20.114Z + 2024-03-22T13:06:36.112Z http://hits-mbm-dev.github.io/kimmdy/_reference/topology.utils.html - 2024-03-19T10:43:19.854Z + 2024-03-22T13:06:35.848Z http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/write-plugin.html - 2024-03-19T10:42:20.654Z + 2024-03-22T13:05:41.436Z http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/index.html - 2024-03-19T10:42:20.654Z + 2024-03-22T13:05:41.436Z http://hits-mbm-dev.github.io/kimmdy/guide/references/cmd_ref.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/guide/how-to/install-ml-plugins.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/guide/how-to/contribute.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/guide/how-to/reaction_only.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z http://hits-mbm-dev.github.io/kimmdy/guide/explanation/topology.html - 2024-03-19T10:42:20.646Z + 2024-03-22T13:05:41.428Z