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