source: utils/Python/HOWTO-boxmaker@ 23d10f

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 Candidate_v1.7.0 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 23d10f was 9fd196, checked in by Frederik Heber <heber@…>, 14 years ago

Added bash_completion file.

  • use as . utils/Bash/bash_completion, installed in bin folder.
  • moved all python files in utils into subfolder Python therein.
  • We scan molecuilder's help output for the present actions and return in COMPREPLY, fully capable of giving option to last action and all available actions in any other case.
  • we expand files if no "--" is given.
  • TESTFIX: Python/BoxMaker needs to call boxmaker.py from utils/Python.
  • Property mode set to 100644
File size: 3.8 KB
RevLine 
[b82ede]1Boxmaker creates boxes of specific density filled with molecules
2
3==========================================================
4
5Usage:
6 boxmaker.py <basename> [option1 value1...]
7
8 boxmaker.py <basename> [+boolean_option -other_boolean_option]
9 same as
10 boxmaker.py <basename> [boolean_option on other_boolean_option off]
11
12==========================================================
13
14If existing boxmaker reads boxmaker.<basename> as configuration file. The
15syntax used is:
16
17# comment line
18option1 = value1
19option2 = value2
20...
21
22Note that shortcuts rather than actual option names can be used at all times,
23however this is not recommended in the configuration file for clarities sake.
24
25Options with units will be converted to the system specified by the
26<basename>.tremolo file if autodim=on. If the value is preceeded by ! the unit
27convertion can be switched off for this specific value.
28
29o List of name-value options:
30
31tremofiledir
32 (Optional if autodim=off)
33 Shortcut: tf
34 Default: ./
35
36 <basename>.tremolo is needed to dertermine the targed system of units. tf
37 specifies where to find the file.
38
39potentialsfiledir
40 Shortcut: pf
41 Default: ./
42
43 <basename>.potentials is needed internally for MoleCuilders element
44 mapping. Also, if automass=on, it's needed to automatically determine the
45 input molecules molar mass.
46 pf specifies where to find the file.
47
48outfilename
49 Shortcut: o
50 Default: out
51
52 The name stem of the output files. By default its out.xyz and out.data
53
54source
55 Shortcut: i
56 Default: None
57
58 The full path to the molecule file used to fill the box. Supports any format
59 MoleCuilder does.
60
61molarmass
62 (Optional if automass=on)
63 Shortcut: m
64 Default: None
65
66 Specify the molar mass of the input molecule. Value with unit.
67
68 E.g.: molarmass = 23.45e-3 kg/mol
69 E.g.: molarmass = !66.3333
70
71density
72 Shortcut: rho
73 Default: None
74
75 Specify the desired density of the box. Value with unit.
76
77temp
78 (Optional)
79 Shortcut: t
80 Default: None
81
82 If specified and postprocessing is on, the resulting data-file is given an
83 additional
84
85 # INPUTCONV temp <converted value>
86
87 header-line. Value with unit.
88
89number
90 Shortcut: n
91 Default: 1000
92
93 How many molecules is the box supposed to contain? Might be internally
94 changed if cubicdomain=on.
95
96 If number is a vector the box is filled by x*y*z molecules, ignoring
97 the option cubicdomain.
98
99 E.g.: number = 4 3 9
100
101o List of boolean options:
102
103cubicdomain
104 Shortcut: cd
105 Default: on
106
107 If on the box is filled with n*n*n molecules where n is the nearest power
108 of 3 to fit number. Ignored if number is a vector.
109
110cubiccell
111 Shortcut: cc
112 Default: off
113
114 Normally the cuboid of an elementary cell is the input molecules bounding
115 box, scaled to fit the desired molecular volume. If on the elementary cells
116 strictly cubic. Its the only way to archive a cubic simulation area (given
117 cubicdomain is on), but its very likely that molecules will overlap unless
118 its near cubic.
119
120autorotate
121 Shortcut: ar
122 Default: off
123
124 Uses MoleCuilder to rotate the input molecule in a way such that the
125 bouding box' volume is minimized, leading to a higher possible density
126 without overlap.
127
128autodim
129 Shortcut: ad
130 Default: on
131
132 If on units will be converted to the system specified in the tremolo-file.
133
134postprocess
135 Shortcut: pp
136 Default: on
137
138 Adds "# INPUTCONV shift center" to the resulting data file. If a
139 temperature is given its added as well.
140
141automass
142 Shortcut: am
143 Default: on
144
145 If specified boxmaker tries to determine the molar mass using the
146 <basename>.potentials file.
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