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====== Jacapo Object ======
Python interface to the Fortran DACAPO code.
<html><head><title>Python: module ase.calculators.jacapo.jacapo</title></head><body bgcolor="#f0f0f8"><br>
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<font color="#000000" face="helvetica, arial"><a name="Jacapo">class <strong>Jacapo</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan="2"><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan="2"><tt>Python&nbsp;interface&nbsp;to&nbsp;the&nbsp;Fortran&nbsp;DACAPO&nbsp;code<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Jacapo-__del__"><strong>__del__</strong></a>(self)</dt><dd><tt>If&nbsp;calculator&nbsp;is&nbsp;deleted&nbsp;try&nbsp;to&nbsp;stop&nbsp;dacapo&nbsp;program</tt></dd></dl>

<dl><dt><a name="Jacapo-__init__"><strong>__init__</strong></a>(self, nc<font color="#909090">='out.nc'</font>, outnc<font color="#909090">=None</font>, deletenc<font color="#909090">=False</font>, debug<font color="#909090">=30</font>, stay_alive<font color="#909090">=False</font>, **kwargs)</dt><dd><tt>Initialize&nbsp;the&nbsp;<a href="#Jacapo">Jacapo</a>&nbsp;calculator<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;nc&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;output&nbsp;netcdf&nbsp;file,&nbsp;or&nbsp;input&nbsp;file&nbsp;if&nbsp;nc&nbsp;already&nbsp;exists<br>
&nbsp;<br>
&nbsp;&nbsp;outnc&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;output&nbsp;file.&nbsp;by&nbsp;default&nbsp;equal&nbsp;to&nbsp;nc<br>
&nbsp;<br>
&nbsp;&nbsp;deletenc&nbsp;:&nbsp;Boolean<br>
&nbsp;&nbsp;&nbsp;determines&nbsp;whether&nbsp;the&nbsp;ncfile&nbsp;is&nbsp;deleted&nbsp;on&nbsp;initialization<br>&nbsp;&nbsp;&nbsp;so&nbsp;a&nbsp;fresh&nbsp;run&nbsp;occurs.&nbsp;If&nbsp;True,&nbsp;the&nbsp;ncfile&nbsp;is&nbsp;deleted&nbsp;if<br>
&nbsp;&nbsp;&nbsp;it&nbsp;exists.<br>
&nbsp;<br>
&nbsp;&nbsp;debug&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;logging&nbsp;debug&nbsp;level.<br>
&nbsp;<br>
Valid&nbsp;kwargs:<br>
&nbsp;<br>
&nbsp;&nbsp;atoms&nbsp;:&nbsp;ASE.Atoms&nbsp;instance<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms&nbsp;is&nbsp;an&nbsp;ase.Atoms&nbsp;object&nbsp;that&nbsp;will&nbsp;be&nbsp;attached<br>
&nbsp;&nbsp;&nbsp;&nbsp;to&nbsp;this&nbsp;calculator.<br>
&nbsp;<br>
&nbsp;&nbsp;pw&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;sets&nbsp;planewave&nbsp;cutoff<br>
&nbsp;<br>
&nbsp;&nbsp;dw&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;sets&nbsp;density&nbsp;cutoff<br>
&nbsp;<br>
&nbsp;&nbsp;kpts&nbsp;:&nbsp;iterable<br>
&nbsp;&nbsp;&nbsp;&nbsp;set&nbsp;chadi-cohen,&nbsp;monkhorst-pack&nbsp;kpt&nbsp;grid,<br>
&nbsp;&nbsp;&nbsp;&nbsp;e.g.&nbsp;kpts&nbsp;=&nbsp;(2,2,1)&nbsp;or&nbsp;explicit&nbsp;list&nbsp;of&nbsp;kpts<br>
&nbsp;<br>
&nbsp;&nbsp;spinpol&nbsp;:&nbsp;Boolean<br>
&nbsp;&nbsp;&nbsp;&nbsp;sets&nbsp;whether&nbsp;spin-polarization&nbsp;is&nbsp;used&nbsp;or&nbsp;not.<br>
&nbsp;<br>
&nbsp;&nbsp;fixmagmom&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;set&nbsp;the&nbsp;magnetic&nbsp;moment&nbsp;of&nbsp;the&nbsp;unit&nbsp;cell.&nbsp;only&nbsp;used<br>
&nbsp;&nbsp;&nbsp;&nbsp;in&nbsp;spin&nbsp;polarize&nbsp;calculations<br>
&nbsp;<br>
&nbsp;&nbsp;ft&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;set&nbsp;the&nbsp;Fermi&nbsp;temperature&nbsp;used&nbsp;in&nbsp;occupation&nbsp;smearing<br>
&nbsp;<br>
&nbsp;&nbsp;xc&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;set&nbsp;the&nbsp;exchange-correlation&nbsp;functional.<br>
&nbsp;&nbsp;&nbsp;&nbsp;one&nbsp;of&nbsp;['PZ','VWN','PW91','PBE','RPBE','revPBE'],<br>
&nbsp;<br>
&nbsp;&nbsp;dipole<br>
&nbsp;&nbsp;&nbsp;&nbsp;boolean<br>
&nbsp;&nbsp;&nbsp;&nbsp;turn&nbsp;the&nbsp;dipole&nbsp;correction&nbsp;on&nbsp;(True)&nbsp;or&nbsp;off&nbsp;(False)<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;or:<br>
&nbsp;&nbsp;&nbsp;&nbsp;dictionary&nbsp;of&nbsp;parameters&nbsp;to&nbsp;fine-tune&nbsp;behavior<br>
&nbsp;&nbsp;&nbsp;&nbsp;{'status':False,<br>
&nbsp;&nbsp;&nbsp;&nbsp;'mixpar':0.2,<br>
&nbsp;&nbsp;&nbsp;&nbsp;'initval':0.0,<br>
&nbsp;&nbsp;&nbsp;&nbsp;'adddipfield':0.0,<br>
&nbsp;&nbsp;&nbsp;&nbsp;'position':None}<br>
&nbsp;<br>
&nbsp;&nbsp;nbands&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;set&nbsp;the&nbsp;number&nbsp;of&nbsp;bands<br>
&nbsp;<br>
&nbsp;&nbsp;symmetry&nbsp;:&nbsp;Boolean<br>
&nbsp;&nbsp;&nbsp;&nbsp;Turn&nbsp;symmetry&nbsp;reduction&nbsp;on&nbsp;(True)&nbsp;or&nbsp;off&nbsp;(False)<br>
&nbsp;<br>
&nbsp;&nbsp;stress&nbsp;:&nbsp;Boolean<br>
&nbsp;&nbsp;&nbsp;&nbsp;Turn&nbsp;stress&nbsp;calculation&nbsp;on&nbsp;(True)&nbsp;or&nbsp;off&nbsp;(False)<br>
&nbsp;<br>
&nbsp;&nbsp;debug&nbsp;:&nbsp;level&nbsp;for&nbsp;logging<br>
&nbsp;&nbsp;&nbsp;&nbsp;could&nbsp;be&nbsp;something&nbsp;like<br>
&nbsp;&nbsp;&nbsp;&nbsp;logging.DEBUG&nbsp;or&nbsp;an&nbsp;integer&nbsp;0-50.&nbsp;The&nbsp;higher&nbsp;the&nbsp;integer,<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;less&nbsp;information&nbsp;you&nbsp;see&nbsp;set&nbsp;debug&nbsp;level&nbsp;(0&nbsp;=&nbsp;off,&nbsp;10&nbsp;=<br>
&nbsp;&nbsp;&nbsp;&nbsp;extreme)<br>
&nbsp;<br>
Modification&nbsp;of&nbsp;the&nbsp;nc&nbsp;file&nbsp;only&nbsp;occurs&nbsp;at&nbsp;calculate&nbsp;time&nbsp;if&nbsp;needed<br>
&nbsp;<br>
&gt;&gt;&gt;&nbsp;calc&nbsp;=&nbsp;<a href="#Jacapo">Jacapo</a>('CO.nc')<br>
&nbsp;<br>
reads&nbsp;the&nbsp;calculator&nbsp;from&nbsp;CO.nc&nbsp;if&nbsp;it&nbsp;exists&nbsp;or<br>
minimally&nbsp;initializes&nbsp;CO.nc&nbsp;with&nbsp;dimensions&nbsp;if&nbsp;it&nbsp;does&nbsp;not&nbsp;exist.<br>
&nbsp;<br>
&gt;&gt;&gt;&nbsp;calc&nbsp;=&nbsp;<a href="#Jacapo">Jacapo</a>('CO.nc',&nbsp;pw=300)<br>
&nbsp;<br>
reads&nbsp;the&nbsp;calculator&nbsp;from&nbsp;CO.nc&nbsp;or&nbsp;initializes&nbsp;it&nbsp;if<br>
it&nbsp;does&nbsp;not&nbsp;exist&nbsp;and&nbsp;changes&nbsp;the&nbsp;planewave&nbsp;cutoff&nbsp;energy&nbsp;to<br>
300eV<br>
&nbsp;<br>
&nbsp;&gt;&gt;&gt;&nbsp;atoms&nbsp;=&nbsp;<a href="#Jacapo">Jacapo</a>.<a href="#Jacapo-read_atoms">read_atoms</a>('CO.nc')<br>
&nbsp;<br>
returns&nbsp;the&nbsp;atoms&nbsp;in&nbsp;the&nbsp;netcdffile&nbsp;CO.nc,&nbsp;with&nbsp;the&nbsp;calculator<br>
attached&nbsp;to&nbsp;it.<br>
&nbsp;<br>
&gt;&gt;&gt;&nbsp;atoms,&nbsp;calc&nbsp;=&nbsp;<a href="#-read">read</a>('CO.nc')</tt></dd></dl>

<dl><dt><a name="Jacapo-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>pretty-print&nbsp;the&nbsp;calculator&nbsp;and&nbsp;atoms.<br>
&nbsp;<br>
we&nbsp;read&nbsp;everything&nbsp;directly&nbsp;from&nbsp;the&nbsp;ncfile&nbsp;to&nbsp;prevent<br>
triggering&nbsp;any&nbsp;calculations</tt></dd></dl>

<dl><dt><a name="Jacapo-atoms_are_equal"><strong>atoms_are_equal</strong></a>(self, atoms)</dt><dd><tt>comparison&nbsp;of&nbsp;atoms&nbsp;to&nbsp;self.<strong>atoms</strong>&nbsp;using&nbsp;tolerances&nbsp;to&nbsp;account<br>
for&nbsp;float/double&nbsp;differences&nbsp;and&nbsp;float&nbsp;math.</tt></dd></dl>

<dl><dt><a name="Jacapo-attach_child"><strong>attach_child</strong></a>(self, child)</dt></dl>

<dl><dt><a name="Jacapo-calculate"><strong>calculate</strong></a>(self)</dt><dd><tt>run&nbsp;a&nbsp;calculation.<br>
&nbsp;<br>
you&nbsp;have&nbsp;to&nbsp;be&nbsp;a&nbsp;little&nbsp;careful&nbsp;with&nbsp;code&nbsp;in&nbsp;here.&nbsp;Use&nbsp;the<br>
calculation_required&nbsp;function&nbsp;to&nbsp;tell&nbsp;if&nbsp;a&nbsp;calculation&nbsp;is<br>
required.&nbsp;It&nbsp;is&nbsp;assumed&nbsp;here&nbsp;that&nbsp;if&nbsp;you&nbsp;call&nbsp;this,&nbsp;you&nbsp;mean<br>
it.</tt></dd></dl>

<dl><dt><a name="Jacapo-calculation_required"><strong>calculation_required</strong></a>(self, atoms<font color="#909090">=None</font>, quantities<font color="#909090">=None</font>)</dt><dd><tt>determines&nbsp;if&nbsp;a&nbsp;calculation&nbsp;is&nbsp;needed.<br>
&nbsp;<br>
return&nbsp;True&nbsp;if&nbsp;a&nbsp;calculation&nbsp;is&nbsp;needed&nbsp;to&nbsp;get&nbsp;up&nbsp;to&nbsp;date&nbsp;data.<br>
return&nbsp;False&nbsp;if&nbsp;no&nbsp;calculation&nbsp;is&nbsp;needed.<br>
&nbsp;<br>
quantities&nbsp;is&nbsp;here&nbsp;because&nbsp;of&nbsp;the&nbsp;ase&nbsp;interface.</tt></dd></dl>

<dl><dt><a name="Jacapo-delete_ncattdimvar"><strong>delete_ncattdimvar</strong></a>(self, ncf, ncattrs<font color="#909090">=None</font>, ncdims<font color="#909090">=None</font>, ncvars<font color="#909090">=None</font>)</dt><dd><tt>helper&nbsp;function&nbsp;to&nbsp;delete&nbsp;attributes,<br>
dimensions&nbsp;and&nbsp;variables&nbsp;in&nbsp;a&nbsp;netcdffile<br>
&nbsp;<br>
this&nbsp;functionality&nbsp;is&nbsp;not&nbsp;implemented&nbsp;for&nbsp;some&nbsp;reason&nbsp;in<br>
netcdf,&nbsp;so&nbsp;the&nbsp;only&nbsp;way&nbsp;to&nbsp;do&nbsp;this&nbsp;is&nbsp;to&nbsp;copy&nbsp;all&nbsp;the<br>
attributes,&nbsp;dimensions,&nbsp;and&nbsp;variables&nbsp;to&nbsp;a&nbsp;new&nbsp;file,&nbsp;excluding<br>
the&nbsp;ones&nbsp;you&nbsp;want&nbsp;to&nbsp;delete&nbsp;and&nbsp;then&nbsp;rename&nbsp;the&nbsp;new&nbsp;file.<br>
&nbsp;<br>
if&nbsp;you&nbsp;delete&nbsp;a&nbsp;dimension,&nbsp;all&nbsp;variables&nbsp;with&nbsp;that&nbsp;dimension<br>
are&nbsp;also&nbsp;deleted.</tt></dd></dl>

<dl><dt><a name="Jacapo-execute_external_dynamics"><strong>execute_external_dynamics</strong></a>(self, nc<font color="#909090">=None</font>, txt<font color="#909090">=None</font>, stoppfile<font color="#909090">='stop'</font>, stopprogram<font color="#909090">=None</font>)</dt><dd><tt>Implementation&nbsp;of&nbsp;the&nbsp;stay&nbsp;alive&nbsp;functionality&nbsp;with&nbsp;socket<br>
communication&nbsp;between&nbsp;dacapo&nbsp;and&nbsp;python.&nbsp;&nbsp;Known&nbsp;limitations:<br>
It&nbsp;is&nbsp;not&nbsp;possible&nbsp;to&nbsp;start&nbsp;2&nbsp;independent&nbsp;Dacapo&nbsp;calculators<br>
from&nbsp;the&nbsp;same&nbsp;python&nbsp;process,&nbsp;since&nbsp;the&nbsp;python&nbsp;PID&nbsp;is&nbsp;used&nbsp;as<br>
identifier&nbsp;for&nbsp;the&nbsp;script[PID].py&nbsp;file.</tt></dd></dl>

<dl><dt><a name="Jacapo-execute_parent_calculation"><strong>execute_parent_calculation</strong></a>(self)</dt><dd><tt>Implementation&nbsp;of&nbsp;an&nbsp;extra&nbsp;level&nbsp;of&nbsp;parallelization,&nbsp;where&nbsp;one&nbsp;jacapo&nbsp;calculator&nbsp;spawns&nbsp;several<br>
dacapo.run&nbsp;processes.&nbsp;This&nbsp;is&nbsp;used&nbsp;for&nbsp;NEBs&nbsp;parallelized&nbsp;over&nbsp;images.</tt></dd></dl>

<dl><dt><a name="Jacapo-get"><strong>get</strong></a>(self, *args)</dt><dd><tt>get&nbsp;values&nbsp;for&nbsp;args.<br>
&nbsp;<br>
e.g.&nbsp;calc.<a href="#Jacapo-get">get</a>('nbands')</tt></dd></dl>

<dl><dt><a name="Jacapo-get_ados"><strong>get_ados</strong></a>(self, **kwargs)</dt><dd><tt>attempt&nbsp;at&nbsp;maintaining&nbsp;backward&nbsp;compatibility&nbsp;with&nbsp;get_ados<br>
returning&nbsp;data<br>
&nbsp;<br>
Now&nbsp;when&nbsp;we&nbsp;call&nbsp;calc.<a href="#Jacapo-get_ados">get_ados</a>()&nbsp;it&nbsp;will&nbsp;return&nbsp;settings,<br>
&nbsp;<br>
and&nbsp;calc.<a href="#Jacapo-get_ados">get_ados</a>(atoms=[],...)&nbsp;should&nbsp;return&nbsp;data</tt></dd></dl>

<dl><dt><a name="Jacapo-get_ados_data"><strong>get_ados_data</strong></a>(self, atoms, orbitals, cutoff, spin)</dt><dd><tt>get&nbsp;atom&nbsp;projected&nbsp;data<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;atoms<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;list&nbsp;of&nbsp;atom&nbsp;indices&nbsp;(integers)<br>
&nbsp;<br>
&nbsp;&nbsp;orbitals<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;list&nbsp;of&nbsp;strings<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;['s','p','d'],<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;['px','py','pz']<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;['d_zz',&nbsp;'dxx-yy',&nbsp;'d_xy',&nbsp;'d_xz',&nbsp;'d_yz']<br>
&nbsp;<br>
&nbsp;&nbsp;cutoff&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;cutoff&nbsp;radius&nbsp;you&nbsp;want&nbsp;the&nbsp;results&nbsp;for&nbsp;'short'&nbsp;or&nbsp;'infinite'<br>
&nbsp;<br>
&nbsp;&nbsp;spin<br>
&nbsp;&nbsp;&nbsp;&nbsp;:&nbsp;list&nbsp;of&nbsp;integers<br>
&nbsp;&nbsp;&nbsp;&nbsp;spin&nbsp;you&nbsp;want&nbsp;the&nbsp;results&nbsp;for<br>
&nbsp;&nbsp;&nbsp;&nbsp;[0]&nbsp;or&nbsp;[1]&nbsp;or&nbsp;[0,1]&nbsp;for&nbsp;both<br>
&nbsp;<br>
returns&nbsp;(egrid,&nbsp;ados)<br>
egrid&nbsp;has&nbsp;the&nbsp;fermi&nbsp;level&nbsp;at&nbsp;0&nbsp;eV</tt></dd></dl>

<dl><dt><a name="Jacapo-get_all_eigenvalues"><strong>get_all_eigenvalues</strong></a>(self, spin<font color="#909090">=0</font>)</dt><dd><tt>return&nbsp;all&nbsp;the&nbsp;eigenvalues&nbsp;at&nbsp;all&nbsp;the&nbsp;kpoints&nbsp;for&nbsp;a&nbsp;spin.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;spin&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;which&nbsp;spin&nbsp;the&nbsp;eigenvalues&nbsp;are&nbsp;for</tt></dd></dl>

<dl><dt><a name="Jacapo-get_ascii_debug"><strong>get_ascii_debug</strong></a>(self)</dt><dd><tt>Return&nbsp;the&nbsp;debug&nbsp;settings&nbsp;in&nbsp;Dacapo</tt></dd></dl>

<dl><dt><a name="Jacapo-get_atoms"><strong>get_atoms</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;atoms&nbsp;attached&nbsp;to&nbsp;a&nbsp;calculator()</tt></dd></dl>

<dl><dt><a name="Jacapo-get_bz_k_points"><strong>get_bz_k_points</strong></a>(self)</dt><dd><tt>return&nbsp;list&nbsp;of&nbsp;kpoints&nbsp;in&nbsp;the&nbsp;Brillouin&nbsp;zone</tt></dd></dl>

<dl><dt><a name="Jacapo-get_calculate_stress"><strong>get_calculate_stress</strong></a>(self)</dt><dd><tt>return&nbsp;whether&nbsp;stress&nbsp;is&nbsp;calculated&nbsp;or&nbsp;not</tt></dd></dl>

<dl><dt><a name="Jacapo-get_cd"><strong>get_cd</strong></a> = <a href="#Jacapo-get_charge_density">get_charge_density</a>(self, spin<font color="#909090">=0</font>)</dt></dl>

<dl><dt><a name="Jacapo-get_charge_density"><strong>get_charge_density</strong></a>(self, spin<font color="#909090">=0</font>)</dt><dd><tt>return&nbsp;x,y,z,charge&nbsp;density&nbsp;data<br>
&nbsp;<br>
x,y,z&nbsp;are&nbsp;grids&nbsp;sampling&nbsp;the&nbsp;unit&nbsp;cell<br>
cd&nbsp;is&nbsp;the&nbsp;charge&nbsp;density&nbsp;data<br>
&nbsp;<br>
netcdf&nbsp;documentation::<br>
&nbsp;<br>
&nbsp;&nbsp;ChargeDensity(number_of_spin,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;hardgrid_dim3,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;hardgrid_dim2,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;hardgrid_dim1)<br>
&nbsp;&nbsp;ChargeDensity:Description&nbsp;=&nbsp;"realspace&nbsp;charge&nbsp;density"&nbsp;;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ChargeDensity:unit&nbsp;=&nbsp;"-e/A^3"&nbsp;;</tt></dd></dl>

<dl><dt><a name="Jacapo-get_charge_mixing"><strong>get_charge_mixing</strong></a>(self)</dt><dd><tt>return&nbsp;charge&nbsp;mixing&nbsp;parameters</tt></dd></dl>

<dl><dt><a name="Jacapo-get_convergence"><strong>get_convergence</strong></a>(self)</dt><dd><tt>return&nbsp;convergence&nbsp;settings&nbsp;for&nbsp;Dacapo</tt></dd></dl>

<dl><dt><a name="Jacapo-get_debug"><strong>get_debug</strong></a>(self)</dt><dd><tt>Return&nbsp;the&nbsp;python&nbsp;logging&nbsp;level</tt></dd></dl>

<dl><dt><a name="Jacapo-get_decoupling"><strong>get_decoupling</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;electrostatic&nbsp;decoupling&nbsp;parameters</tt></dd></dl>

<dl><dt><a name="Jacapo-get_dipole"><strong>get_dipole</strong></a>(self)</dt><dd><tt>return&nbsp;dictionary&nbsp;of&nbsp;parameters&nbsp;if&nbsp;the&nbsp;DipoleCorrection&nbsp;was&nbsp;used</tt></dd></dl>

<dl><dt><a name="Jacapo-get_dipole_moment"><strong>get_dipole_moment</strong></a>(self, atoms<font color="#909090">=None</font>)</dt><dd><tt>return&nbsp;dipole&nbsp;moment&nbsp;of&nbsp;unit&nbsp;cell<br>
&nbsp;<br>
Defined&nbsp;by&nbsp;the&nbsp;vector&nbsp;connecting&nbsp;the&nbsp;center&nbsp;of&nbsp;electron&nbsp;charge<br>
density&nbsp;to&nbsp;the&nbsp;center&nbsp;of&nbsp;nuclear&nbsp;charge&nbsp;density.<br>
&nbsp;<br>
Units&nbsp;=&nbsp;eV*angstrom<br>
&nbsp;<br>
1&nbsp;Debye&nbsp;=&nbsp;0.208194&nbsp;eV*angstrom</tt></dd></dl>

<dl><dt><a name="Jacapo-get_dw"><strong>get_dw</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;density&nbsp;wave&nbsp;cutoff</tt></dd></dl>

<dl><dt><a name="Jacapo-get_ef"><strong>get_ef</strong></a> = <a href="#Jacapo-get_fermi_level">get_fermi_level</a>(self)</dt></dl>

<dl><dt><a name="Jacapo-get_effective_potential"><strong>get_effective_potential</strong></a>(self, spin<font color="#909090">=1</font>)</dt><dd><tt>returns&nbsp;the&nbsp;realspace&nbsp;local&nbsp;effective&nbsp;potential&nbsp;for&nbsp;the&nbsp;spin.<br>
the&nbsp;units&nbsp;of&nbsp;the&nbsp;potential&nbsp;are&nbsp;eV<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;spin&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;specify&nbsp;which&nbsp;spin&nbsp;you&nbsp;want,&nbsp;0&nbsp;or&nbsp;1</tt></dd></dl>

<dl><dt><a name="Jacapo-get_eigenvalues"><strong>get_eigenvalues</strong></a>(self, kpt<font color="#909090">=0</font>, spin<font color="#909090">=0</font>)</dt><dd><tt>return&nbsp;the&nbsp;eigenvalues&nbsp;for&nbsp;a&nbsp;kpt&nbsp;and&nbsp;spin<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;kpt&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;index&nbsp;of&nbsp;the&nbsp;IBZ&nbsp;kpoint<br>
&nbsp;<br>
&nbsp;&nbsp;spin&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;which&nbsp;spin&nbsp;the&nbsp;eigenvalues&nbsp;are&nbsp;for</tt></dd></dl>

<dl><dt><a name="Jacapo-get_electronic_minimization"><strong>get_electronic_minimization</strong></a>(self)</dt><dd><tt>get&nbsp;method&nbsp;and&nbsp;diagonalizations&nbsp;per&nbsp;band&nbsp;for&nbsp;electronic<br>
minimization&nbsp;algorithms</tt></dd></dl>

<dl><dt><a name="Jacapo-get_electronic_temperature"><strong>get_electronic_temperature</strong></a> = <a href="#Jacapo-get_ft">get_ft</a>(self)</dt></dl>

<dl><dt><a name="Jacapo-get_electrostatic_potential"><strong>get_electrostatic_potential</strong></a>(self, spin<font color="#909090">=0</font>)</dt><dd><tt>get&nbsp;electrostatic&nbsp;potential<br>
&nbsp;<br>
Netcdf&nbsp;documentation::<br>
&nbsp;<br>
&nbsp;&nbsp;double&nbsp;ElectrostaticPotential(number_of_spin,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;hardgrid_dim3,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;hardgrid_dim2,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;hardgrid_dim1)&nbsp;;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ElectrostaticPotential:<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Description&nbsp;=&nbsp;"realspace&nbsp;local&nbsp;effective&nbsp;potential"&nbsp;;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;unit&nbsp;=&nbsp;"eV"&nbsp;;</tt></dd></dl>

<dl><dt><a name="Jacapo-get_ensemble_coefficients"><strong>get_ensemble_coefficients</strong></a>(self)</dt><dd><tt>returns&nbsp;exchange&nbsp;correlation&nbsp;ensemble&nbsp;coefficients</tt></dd></dl>

<dl><dt><a name="Jacapo-get_esp"><strong>get_esp</strong></a> = <a href="#Jacapo-get_electrostatic_potential">get_electrostatic_potential</a>(self, spin<font color="#909090">=0</font>)</dt></dl>

<dl><dt><a name="Jacapo-get_external_dipole"><strong>get_external_dipole</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;External&nbsp;dipole&nbsp;settings</tt></dd></dl>

<dl><dt><a name="Jacapo-get_extpot"><strong>get_extpot</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;external&nbsp;potential&nbsp;set&nbsp;in&nbsp;teh&nbsp;calculator</tt></dd></dl>

<dl><dt><a name="Jacapo-get_extracharge"><strong>get_extracharge</strong></a>(self)</dt><dd><tt>Return&nbsp;the&nbsp;extra&nbsp;charge&nbsp;set&nbsp;in&nbsp;teh&nbsp;calculator</tt></dd></dl>

<dl><dt><a name="Jacapo-get_fermi_level"><strong>get_fermi_level</strong></a>(self)</dt><dd><tt>return&nbsp;Fermi&nbsp;level</tt></dd></dl>

<dl><dt><a name="Jacapo-get_fftgrid"><strong>get_fftgrid</strong></a>(self)</dt><dd><tt>return&nbsp;soft&nbsp;and&nbsp;hard&nbsp;fft&nbsp;grids</tt></dd></dl>

<dl><dt><a name="Jacapo-get_fixmagmom"><strong>get_fixmagmom</strong></a>(self)</dt><dd><tt>returns&nbsp;the&nbsp;value&nbsp;of&nbsp;FixedMagneticMoment</tt></dd></dl>

<dl><dt><a name="Jacapo-get_forces"><strong>get_forces</strong></a>(self, atoms<font color="#909090">=None</font>)</dt><dd><tt>Calculate&nbsp;atomic&nbsp;forces</tt></dd></dl>

<dl><dt><a name="Jacapo-get_ft"><strong>get_ft</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;FermiTemperature&nbsp;used&nbsp;in&nbsp;the&nbsp;calculation</tt></dd></dl>

<dl><dt><a name="Jacapo-get_ibz_k_points"><strong>get_ibz_k_points</strong></a> = <a href="#Jacapo-get_ibz_kpoints">get_ibz_kpoints</a>(self)</dt></dl>

<dl><dt><a name="Jacapo-get_ibz_kpoints"><strong>get_ibz_kpoints</strong></a>(self)</dt><dd><tt>return&nbsp;list&nbsp;of&nbsp;kpoints&nbsp;in&nbsp;the&nbsp;irreducible&nbsp;brillouin&nbsp;zone</tt></dd></dl>

<dl><dt><a name="Jacapo-get_k_point_weights"><strong>get_k_point_weights</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;weights&nbsp;on&nbsp;the&nbsp;IBZ&nbsp;kpoints</tt></dd></dl>

<dl><dt><a name="Jacapo-get_kpts"><strong>get_kpts</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;BZ&nbsp;kpts</tt></dd></dl>

<dl><dt><a name="Jacapo-get_kpts_type"><strong>get_kpts_type</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;kpt&nbsp;grid&nbsp;type</tt></dd></dl>

<dl><dt><a name="Jacapo-get_magnetic_moment"><strong>get_magnetic_moment</strong></a>(self, atoms<font color="#909090">=None</font>)</dt><dd><tt>calculates&nbsp;the&nbsp;magnetic&nbsp;moment&nbsp;(Bohr-magnetons)&nbsp;of&nbsp;the&nbsp;supercell</tt></dd></dl>

<dl><dt><a name="Jacapo-get_magnetic_moments"><strong>get_magnetic_moments</strong></a>(self, atoms<font color="#909090">=None</font>)</dt><dd><tt>return&nbsp;magnetic&nbsp;moments&nbsp;on&nbsp;each&nbsp;atom&nbsp;after&nbsp;the&nbsp;calculation&nbsp;is<br>
run</tt></dd></dl>

<dl><dt><a name="Jacapo-get_mdos"><strong>get_mdos</strong></a>(self)</dt><dd><tt>return&nbsp;multicentered&nbsp;projected&nbsp;dos&nbsp;parameters</tt></dd></dl>

<dl><dt><a name="Jacapo-get_mdos_data"><strong>get_mdos_data</strong></a>(self, spin<font color="#909090">=0</font>, cutoffradius<font color="#909090">='infinite'</font>)</dt><dd><tt>returns&nbsp;data&nbsp;from&nbsp;multicentered&nbsp;projection<br>
&nbsp;<br>
&nbsp;<br>
returns&nbsp;(mdos,&nbsp;rotmat)<br>
&nbsp;<br>
the&nbsp;rotation&nbsp;matrices&nbsp;are&nbsp;retrieved&nbsp;from&nbsp;the&nbsp;text&nbsp;file.&nbsp;I&nbsp;am<br>
not&nbsp;sure&nbsp;what&nbsp;you&nbsp;would&nbsp;do&nbsp;with&nbsp;these,&nbsp;but&nbsp;there&nbsp;was&nbsp;a&nbsp;note<br>
about&nbsp;them&nbsp;in&nbsp;the&nbsp;old&nbsp;documentation&nbsp;so&nbsp;I&nbsp;put&nbsp;the&nbsp;code&nbsp;to<br>
retrieve&nbsp;them&nbsp;here.&nbsp;the&nbsp;syntax&nbsp;for&nbsp;the&nbsp;return&nbsp;value&nbsp;is:<br>
rotmat[atom#][label]&nbsp;returns&nbsp;the&nbsp;rotation&nbsp;matrix&nbsp;for&nbsp;the<br>
center&nbsp;on&nbsp;the&nbsp;atom#&nbsp;for&nbsp;label.&nbsp;I&nbsp;do&nbsp;not&nbsp;not&nbsp;know&nbsp;what&nbsp;the<br>
label&nbsp;refers&nbsp;to.</tt></dd></dl>

<dl><dt><a name="Jacapo-get_nbands"><strong>get_nbands</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;number&nbsp;of&nbsp;bands&nbsp;used&nbsp;in&nbsp;the&nbsp;calculation</tt></dd></dl>

<dl><dt><a name="Jacapo-get_nc"><strong>get_nc</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;ncfile&nbsp;used&nbsp;for&nbsp;output</tt></dd></dl>

<dl><dt><a name="Jacapo-get_ncoutput"><strong>get_ncoutput</strong></a>(self)</dt><dd><tt>returns&nbsp;the&nbsp;control&nbsp;variables&nbsp;for&nbsp;the&nbsp;ncfile</tt></dd></dl>

<dl><dt><a name="Jacapo-get_number_of_bands"><strong>get_number_of_bands</strong></a> = <a href="#Jacapo-get_nbands">get_nbands</a>(self)</dt></dl>

<dl><dt><a name="Jacapo-get_number_of_electrons"><strong>get_number_of_electrons</strong></a> = <a href="#Jacapo-get_valence">get_valence</a>(self, atoms<font color="#909090">=None</font>)</dt></dl>

<dl><dt><a name="Jacapo-get_number_of_grid_points"><strong>get_number_of_grid_points</strong></a>(self)</dt><dd><tt>return&nbsp;soft&nbsp;fft&nbsp;grid</tt></dd></dl>

<dl><dt><a name="Jacapo-get_number_of_iterations"><strong>get_number_of_iterations</strong></a>(self)</dt></dl>

<dl><dt><a name="Jacapo-get_number_of_spins"><strong>get_number_of_spins</strong></a>(self)</dt><dd><tt>if&nbsp;spin-polarized&nbsp;returns&nbsp;2,&nbsp;if&nbsp;not&nbsp;returns&nbsp;1</tt></dd></dl>

<dl><dt><a name="Jacapo-get_occ"><strong>get_occ</strong></a> = <a href="#Jacapo-get_occupation_numbers">get_occupation_numbers</a>(self, kpt<font color="#909090">=0</font>, spin<font color="#909090">=0</font>)</dt></dl>

<dl><dt><a name="Jacapo-get_occupation_numbers"><strong>get_occupation_numbers</strong></a>(self, kpt<font color="#909090">=0</font>, spin<font color="#909090">=0</font>)</dt><dd><tt>return&nbsp;occupancies&nbsp;of&nbsp;eigenstates&nbsp;for&nbsp;a&nbsp;kpt&nbsp;and&nbsp;spin<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;kpt&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;index&nbsp;of&nbsp;the&nbsp;IBZ&nbsp;kpoint&nbsp;you&nbsp;want&nbsp;the&nbsp;occupation&nbsp;of<br>
&nbsp;<br>
&nbsp;&nbsp;spin&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;or&nbsp;1</tt></dd></dl>

<dl><dt><a name="Jacapo-get_occupationstatistics"><strong>get_occupationstatistics</strong></a>(self)</dt><dd><tt>return&nbsp;occupation&nbsp;statistics&nbsp;method</tt></dd></dl>

<dl><dt><a name="Jacapo-get_potential_energy"><strong>get_potential_energy</strong></a>(self, atoms<font color="#909090">=None</font>, force_consistent<font color="#909090">=False</font>)</dt><dd><tt>return&nbsp;the&nbsp;potential&nbsp;energy.</tt></dd></dl>

<dl><dt><a name="Jacapo-get_pseudo_wave_function"><strong>get_pseudo_wave_function</strong></a>(self, band<font color="#909090">=0</font>, kpt<font color="#909090">=0</font>, spin<font color="#909090">=0</font>, pad<font color="#909090">=True</font>)</dt><dd><tt>return&nbsp;the&nbsp;pseudo&nbsp;wavefunction</tt></dd></dl>

<dl><dt><a name="Jacapo-get_pseudopotentials"><strong>get_pseudopotentials</strong></a>(self)</dt><dd><tt>get&nbsp;pseudopotentials&nbsp;set&nbsp;for&nbsp;atoms&nbsp;attached&nbsp;to&nbsp;calculator</tt></dd></dl>

<dl><dt><a name="Jacapo-get_psp"><strong>get_psp</strong></a>(self, sym<font color="#909090">=None</font>, z<font color="#909090">=None</font>)</dt><dd><tt>get&nbsp;the&nbsp;pseudopotential&nbsp;filename&nbsp;from&nbsp;the&nbsp;psp&nbsp;database<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;sym&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;chemical&nbsp;symbol&nbsp;of&nbsp;the&nbsp;species<br>
&nbsp;<br>
&nbsp;&nbsp;z&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;atomic&nbsp;number&nbsp;of&nbsp;the&nbsp;species<br>
&nbsp;<br>
&nbsp;<br>
you&nbsp;can&nbsp;only&nbsp;specify&nbsp;sym&nbsp;or&nbsp;z.&nbsp;Returns&nbsp;the&nbsp;pseudopotential<br>
filename,&nbsp;not&nbsp;the&nbsp;full&nbsp;path.</tt></dd></dl>

<dl><dt><a name="Jacapo-get_psp_nuclear_charge"><strong>get_psp_nuclear_charge</strong></a>(self, psp)</dt><dd><tt>get&nbsp;the&nbsp;nuclear&nbsp;charge&nbsp;of&nbsp;the&nbsp;atom&nbsp;from&nbsp;teh&nbsp;psp-file.<br>
&nbsp;<br>
This&nbsp;is&nbsp;not&nbsp;the&nbsp;same&nbsp;as&nbsp;the&nbsp;atomic&nbsp;number,&nbsp;nor&nbsp;is&nbsp;it<br>
necessarily&nbsp;the&nbsp;negative&nbsp;of&nbsp;the&nbsp;number&nbsp;of&nbsp;valence&nbsp;electrons,<br>
since&nbsp;a&nbsp;psp&nbsp;may&nbsp;be&nbsp;an&nbsp;ion.&nbsp;this&nbsp;function&nbsp;is&nbsp;needed&nbsp;to&nbsp;compute<br>
centers&nbsp;of&nbsp;ion&nbsp;charge&nbsp;for&nbsp;the&nbsp;dipole&nbsp;moment&nbsp;calculation.<br>
&nbsp;<br>
We&nbsp;read&nbsp;in&nbsp;the&nbsp;valence&nbsp;ion&nbsp;configuration&nbsp;from&nbsp;the&nbsp;psp&nbsp;file&nbsp;and<br>
add&nbsp;up&nbsp;the&nbsp;charges&nbsp;in&nbsp;each&nbsp;shell.</tt></dd></dl>

<dl><dt><a name="Jacapo-get_psp_valence"><strong>get_psp_valence</strong></a>(self, psp)</dt><dd><tt>get&nbsp;the&nbsp;psp&nbsp;valence&nbsp;charge&nbsp;on&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;pspfile.</tt></dd></dl>

<dl><dt><a name="Jacapo-get_pw"><strong>get_pw</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;planewave&nbsp;cutoff&nbsp;used</tt></dd></dl>

<dl><dt><a name="Jacapo-get_reciprocal_bloch_function"><strong>get_reciprocal_bloch_function</strong></a>(self, band<font color="#909090">=0</font>, kpt<font color="#909090">=0</font>, spin<font color="#909090">=0</font>)</dt><dd><tt>return&nbsp;the&nbsp;reciprocal&nbsp;bloch&nbsp;function.&nbsp;Need&nbsp;for&nbsp;<a href="#Jacapo">Jacapo</a><br>
Wannier&nbsp;class.</tt></dd></dl>

<dl><dt><a name="Jacapo-get_reciprocal_fft_index"><strong>get_reciprocal_fft_index</strong></a>(self, kpt<font color="#909090">=0</font>)</dt><dd><tt>return&nbsp;the&nbsp;Wave&nbsp;Function&nbsp;FFT&nbsp;Index</tt></dd></dl>

<dl><dt><a name="Jacapo-get_scratch"><strong>get_scratch</strong></a>(self)</dt><dd><tt>finds&nbsp;an&nbsp;appropriate&nbsp;scratch&nbsp;directory&nbsp;for&nbsp;the&nbsp;calculation</tt></dd></dl>

<dl><dt><a name="Jacapo-get_spin_polarized"><strong>get_spin_polarized</strong></a>(self)</dt><dd><tt>Return&nbsp;True&nbsp;if&nbsp;calculate&nbsp;is&nbsp;spin-polarized&nbsp;or&nbsp;False&nbsp;if&nbsp;not</tt></dd></dl>

<dl><dt><a name="Jacapo-get_spinpol"><strong>get_spinpol</strong></a>(self)</dt><dd><tt>Returns&nbsp;the&nbsp;spin&nbsp;polarization&nbsp;setting,&nbsp;either&nbsp;True&nbsp;or&nbsp;False</tt></dd></dl>

<dl><dt><a name="Jacapo-get_status"><strong>get_status</strong></a>(self)</dt><dd><tt>get&nbsp;status&nbsp;of&nbsp;calculation&nbsp;from&nbsp;ncfile.&nbsp;usually&nbsp;one&nbsp;of:<br>
'new',<br>
'aborted'<br>
'running'<br>
'finished'<br>
None</tt></dd></dl>

<dl><dt><a name="Jacapo-get_stay_alive"><strong>get_stay_alive</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;stay&nbsp;alive&nbsp;settings</tt></dd></dl>

<dl><dt><a name="Jacapo-get_stress"><strong>get_stress</strong></a>(self, atoms<font color="#909090">=None</font>)</dt><dd><tt>get&nbsp;stress&nbsp;on&nbsp;the&nbsp;atoms.<br>
&nbsp;<br>
you&nbsp;should&nbsp;have&nbsp;set&nbsp;up&nbsp;the&nbsp;calculation<br>
to&nbsp;calculate&nbsp;stress&nbsp;first.<br>
&nbsp;<br>
returns&nbsp;[sxx,&nbsp;syy,&nbsp;szz,&nbsp;syz,&nbsp;sxz,&nbsp;sxy]</tt></dd></dl>

<dl><dt><a name="Jacapo-get_symmetry"><strong>get_symmetry</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;type&nbsp;of&nbsp;symmetry&nbsp;used</tt></dd></dl>

<dl><dt><a name="Jacapo-get_txt"><strong>get_txt</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;txt&nbsp;file&nbsp;used&nbsp;for&nbsp;output</tt></dd></dl>

<dl><dt><a name="Jacapo-get_ucgrid"><strong>get_ucgrid</strong></a>(self, dims)</dt><dd><tt>Return&nbsp;X,Y,Z&nbsp;grids&nbsp;for&nbsp;uniform&nbsp;sampling&nbsp;of&nbsp;the&nbsp;unit&nbsp;cell<br>
&nbsp;<br>
dims&nbsp;=&nbsp;(n0,n1,n2)<br>
&nbsp;<br>
n0&nbsp;points&nbsp;along&nbsp;unitcell&nbsp;vector&nbsp;0<br>
n1&nbsp;points&nbsp;along&nbsp;unitcell&nbsp;vector&nbsp;1<br>
n2&nbsp;points&nbsp;along&nbsp;unitcell&nbsp;vector&nbsp;2</tt></dd></dl>

<dl><dt><a name="Jacapo-get_valence"><strong>get_valence</strong></a>(self, atoms<font color="#909090">=None</font>)</dt><dd><tt>return&nbsp;the&nbsp;total&nbsp;number&nbsp;of&nbsp;valence&nbsp;electrons&nbsp;for&nbsp;the<br>
atoms.&nbsp;valence&nbsp;electrons&nbsp;are&nbsp;read&nbsp;directly&nbsp;from&nbsp;the<br>
pseudopotentials.<br>
&nbsp;<br>
the&nbsp;psp&nbsp;filenames&nbsp;are&nbsp;stored&nbsp;in&nbsp;the&nbsp;ncfile.&nbsp;They&nbsp;may&nbsp;be&nbsp;just<br>
the&nbsp;name&nbsp;of&nbsp;the&nbsp;file,&nbsp;in&nbsp;which&nbsp;case&nbsp;the&nbsp;psp&nbsp;may&nbsp;exist&nbsp;in&nbsp;the<br>
same&nbsp;directory&nbsp;as&nbsp;the&nbsp;ncfile,&nbsp;or&nbsp;in&nbsp;$DACAPOPATH,&nbsp;or&nbsp;the&nbsp;psp<br>
may&nbsp;be&nbsp;defined&nbsp;by&nbsp;an&nbsp;absolute&nbsp;or&nbsp;relative&nbsp;path.&nbsp;This&nbsp;function<br>
deals&nbsp;with&nbsp;all&nbsp;these&nbsp;possibilities.</tt></dd></dl>

<dl><dt><a name="Jacapo-get_wannier_localization_matrix"><strong>get_wannier_localization_matrix</strong></a>(self, nbands, dirG, kpoint, nextkpoint, G_I, spin)</dt><dd><tt>return&nbsp;wannier&nbsp;localization&nbsp;&nbsp;matrix</tt></dd></dl>

<dl><dt><a name="Jacapo-get_wave_function"><strong>get_wave_function</strong></a>(self, band<font color="#909090">=0</font>, kpt<font color="#909090">=0</font>, spin<font color="#909090">=0</font>)</dt><dd><tt>return&nbsp;the&nbsp;wave&nbsp;function.&nbsp;This&nbsp;is&nbsp;the&nbsp;pseudo&nbsp;wave&nbsp;function<br>
divided&nbsp;by&nbsp;volume.</tt></dd></dl>

<dl><dt><a name="Jacapo-get_wf"><strong>get_wf</strong></a> = <a href="#Jacapo-get_wave_function">get_wave_function</a>(self, band<font color="#909090">=0</font>, kpt<font color="#909090">=0</font>, spin<font color="#909090">=0</font>)</dt></dl>

<dl><dt><a name="Jacapo-get_xc"><strong>get_xc</strong></a>(self)</dt><dd><tt>return&nbsp;the&nbsp;self-consistent&nbsp;exchange-correlation&nbsp;functional&nbsp;used<br>
&nbsp;<br>
returns&nbsp;a&nbsp;string</tt></dd></dl>

<dl><dt><a name="Jacapo-get_xc_energies"><strong>get_xc_energies</strong></a>(self, *functional)</dt><dd><tt>Get&nbsp;energies&nbsp;for&nbsp;different&nbsp;functionals&nbsp;self-consistent&nbsp;and<br>
non-self-consistent.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;functional&nbsp;:&nbsp;strings<br>
&nbsp;&nbsp;&nbsp;&nbsp;some&nbsp;set&nbsp;of&nbsp;'PZ','VWN','PW91','PBE','revPBE',&nbsp;'RPBE'<br>
&nbsp;<br>
This&nbsp;function&nbsp;returns&nbsp;the&nbsp;self-consistent&nbsp;energy&nbsp;and/or<br>
energies&nbsp;associated&nbsp;with&nbsp;various&nbsp;functionals.<br>
The&nbsp;functionals&nbsp;are&nbsp;currently&nbsp;PZ,VWN,PW91,PBE,revPBE,&nbsp;RPBE.<br>
The&nbsp;different&nbsp;energies&nbsp;may&nbsp;be&nbsp;useful&nbsp;for&nbsp;calculating&nbsp;improved<br>
adsorption&nbsp;energies&nbsp;as&nbsp;in&nbsp;B.&nbsp;Hammer,&nbsp;L.B.&nbsp;Hansen&nbsp;and<br>
J.K.&nbsp;Norskov,&nbsp;Phys.&nbsp;Rev.&nbsp;B&nbsp;59,7413.<br>
Examples:<br>
get_xcenergies()&nbsp;#returns&nbsp;all&nbsp;the&nbsp;energies<br>
get_xcenergies('PBE')&nbsp;#&nbsp;returns&nbsp;the&nbsp;PBE&nbsp;total&nbsp;energy<br>
get_xcenergies('PW91','PBE','revPBE')&nbsp;#&nbsp;returns&nbsp;a<br>
#&nbsp;list&nbsp;of&nbsp;energies&nbsp;in&nbsp;the&nbsp;order&nbsp;asked&nbsp;for</tt></dd></dl>

<dl><dt><a name="Jacapo-initial_wannier"><strong>initial_wannier</strong></a>(self, initialwannier, kpointgrid, fixedstates, edf, spin)</dt><dd><tt>return&nbsp;initial&nbsp;wannier</tt></dd></dl>

<dl><dt><a name="Jacapo-initnc"><strong>initnc</strong></a>(self, ncfile<font color="#909090">=None</font>)</dt><dd><tt>create&nbsp;an&nbsp;ncfile&nbsp;with&nbsp;minimal&nbsp;dimensions&nbsp;in&nbsp;it<br>
&nbsp;<br>
this&nbsp;makes&nbsp;sure&nbsp;the&nbsp;dimensions&nbsp;needed&nbsp;for&nbsp;other&nbsp;set&nbsp;functions<br>
exist&nbsp;when&nbsp;needed.</tt></dd></dl>

<dl><dt><a name="Jacapo-read_only_atoms"><strong>read_only_atoms</strong></a>(self, ncfile)</dt><dd><tt>read&nbsp;only&nbsp;the&nbsp;atoms&nbsp;from&nbsp;an&nbsp;existing&nbsp;netcdf&nbsp;file.&nbsp;Used&nbsp;to<br>
initialize&nbsp;a&nbsp;calculator&nbsp;from&nbsp;a&nbsp;ncfilename.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;ncfile&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;name&nbsp;of&nbsp;file&nbsp;to&nbsp;read&nbsp;from.<br>
&nbsp;<br>
return&nbsp;ASE.Atoms&nbsp;with&nbsp;no&nbsp;calculator&nbsp;attached&nbsp;or&nbsp;None&nbsp;if&nbsp;no<br>
atoms&nbsp;found</tt></dd></dl>

<dl><dt><a name="Jacapo-restart"><strong>restart</strong></a>(self)</dt><dd><tt>Restart&nbsp;the&nbsp;calculator&nbsp;by&nbsp;deleting&nbsp;nc&nbsp;dimensions&nbsp;that&nbsp;will<br>
be&nbsp;rewritten&nbsp;on&nbsp;the&nbsp;next&nbsp;calculation.&nbsp;This&nbsp;is&nbsp;sometimes&nbsp;required<br>
when&nbsp;certain&nbsp;dimensions&nbsp;change&nbsp;related&nbsp;to&nbsp;unitcell&nbsp;size&nbsp;changes<br>
planewave/densitywave&nbsp;cutoffs&nbsp;and&nbsp;kpt&nbsp;changes.&nbsp;These&nbsp;can&nbsp;cause<br>
fortran&nbsp;netcdf&nbsp;errors&nbsp;if&nbsp;the&nbsp;data&nbsp;does&nbsp;not&nbsp;match&nbsp;the&nbsp;pre-defined<br>
dimension&nbsp;sizes.<br>
&nbsp;<br>
also&nbsp;delete&nbsp;all&nbsp;the&nbsp;output&nbsp;from&nbsp;previous&nbsp;calculation.</tt></dd></dl>

<dl><dt><a name="Jacapo-set"><strong>set</strong></a>(self, **kwargs)</dt><dd><tt>set&nbsp;a&nbsp;parameter<br>
&nbsp;<br>
parameter&nbsp;is&nbsp;stored&nbsp;in&nbsp;dictionary&nbsp;that&nbsp;is&nbsp;processed&nbsp;later&nbsp;if&nbsp;a<br>
calculation&nbsp;is&nbsp;need.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_ados"><strong>set_ados</strong></a>(self, energywindow<font color="#909090">=(-15, 5)</font>, energywidth<font color="#909090">=0.2</font>, npoints<font color="#909090">=250</font>, cutoff<font color="#909090">=1.0</font>)</dt><dd><tt>setup&nbsp;calculation&nbsp;of&nbsp;atom-projected&nbsp;density&nbsp;of&nbsp;states<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;energywindow&nbsp;:&nbsp;(float,&nbsp;float)<br>
&nbsp;&nbsp;&nbsp;&nbsp;sets&nbsp;(emin,emax)&nbsp;in&nbsp;eV&nbsp;referenced&nbsp;to&nbsp;the&nbsp;Fermi&nbsp;level<br>
&nbsp;<br>
&nbsp;&nbsp;energywidth&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;gaussian&nbsp;used&nbsp;in&nbsp;smearing<br>
&nbsp;<br>
&nbsp;&nbsp;npoints&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;number&nbsp;of&nbsp;points&nbsp;to&nbsp;sample&nbsp;the&nbsp;DOS&nbsp;at<br>
&nbsp;<br>
&nbsp;&nbsp;cutoff&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;cutoff&nbsp;radius&nbsp;in&nbsp;angstroms&nbsp;for&nbsp;the&nbsp;integration.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_ascii_debug"><strong>set_ascii_debug</strong></a>(self, level)</dt><dd><tt>set&nbsp;the&nbsp;debug&nbsp;level&nbsp;for&nbsp;Dacapo<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;level&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;one&nbsp;of&nbsp;'Off',&nbsp;'MediumLevel',&nbsp;'HighLevel'</tt></dd></dl>

<dl><dt><a name="Jacapo-set_atoms"><strong>set_atoms</strong></a>(self, atoms)</dt><dd><tt>attach&nbsp;an&nbsp;atoms&nbsp;to&nbsp;the&nbsp;calculator&nbsp;and&nbsp;update&nbsp;the&nbsp;ncfile<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;atoms<br>
&nbsp;&nbsp;&nbsp;&nbsp;ASE.Atoms&nbsp;instance</tt></dd></dl>

<dl><dt><a name="Jacapo-set_calculate_stress"><strong>set_calculate_stress</strong></a>(self, stress<font color="#909090">=True</font>)</dt><dd><tt>Turn&nbsp;on&nbsp;stress&nbsp;calculation<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;stress&nbsp;:&nbsp;boolean<br>
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Jacapo-set_calculate_stress">set_calculate_stress</a>(True)&nbsp;calculates&nbsp;stress<br>
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Jacapo-set_calculate_stress">set_calculate_stress</a>(False)&nbsp;do&nbsp;not&nbsp;calculate&nbsp;stress</tt></dd></dl>

<dl><dt><a name="Jacapo-set_charge_mixing"><strong>set_charge_mixing</strong></a>(self, method<font color="#909090">='Pulay'</font>, mixinghistory<font color="#909090">=10</font>, mixingcoeff<font color="#909090">=0.1</font>, precondition<font color="#909090">='No'</font>, updatecharge<font color="#909090">='Yes'</font>)</dt><dd><tt>set&nbsp;density&nbsp;mixing&nbsp;method&nbsp;and&nbsp;parameters<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;method&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;'Pulay'&nbsp;for&nbsp;Pulay&nbsp;mixing.&nbsp;only&nbsp;one&nbsp;supported&nbsp;now<br>
&nbsp;<br>
&nbsp;&nbsp;mixinghistory&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;number&nbsp;of&nbsp;iterations&nbsp;to&nbsp;mix<br>
&nbsp;&nbsp;&nbsp;&nbsp;Number&nbsp;of&nbsp;charge&nbsp;residual&nbsp;vectors&nbsp;stored&nbsp;for&nbsp;generating<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;Pulay&nbsp;estimate&nbsp;on&nbsp;the&nbsp;self-consistent&nbsp;charge&nbsp;density,<br>
&nbsp;&nbsp;&nbsp;&nbsp;see&nbsp;Sec.&nbsp;4.2&nbsp;in&nbsp;Kresse/Furthmuller:<br>
&nbsp;&nbsp;&nbsp;&nbsp;Comp.&nbsp;Mat.&nbsp;Sci.&nbsp;6&nbsp;(1996)&nbsp;p34ff<br>
&nbsp;<br>
&nbsp;&nbsp;mixingcoeff&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;Mixing&nbsp;coefficient&nbsp;for&nbsp;Pulay&nbsp;charge&nbsp;mixing,&nbsp;corresponding<br>
&nbsp;&nbsp;&nbsp;&nbsp;to&nbsp;A&nbsp;in&nbsp;G$^1$&nbsp;in&nbsp;Sec.&nbsp;4.2&nbsp;in&nbsp;Kresse/Furthmuller:<br>
&nbsp;&nbsp;&nbsp;&nbsp;Comp.&nbsp;Mat.&nbsp;Sci.&nbsp;6&nbsp;(1996)&nbsp;p34ff<br>
&nbsp;<br>
&nbsp;&nbsp;precondition&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;'Yes'&nbsp;or&nbsp;'No'<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;"Yes"&nbsp;:&nbsp;Kerker&nbsp;preconditiong&nbsp;is&nbsp;used,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;i.e.&nbsp;q$_0$&nbsp;is&nbsp;different&nbsp;from&nbsp;zero,&nbsp;see&nbsp;eq.&nbsp;82<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;in&nbsp;Kresse/Furthmuller:&nbsp;Comp.&nbsp;Mat.&nbsp;Sci.&nbsp;6&nbsp;(1996).<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;q$_0$&nbsp;is&nbsp;fix&nbsp;to&nbsp;give&nbsp;a&nbsp;damping&nbsp;of&nbsp;20<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;of&nbsp;the&nbsp;lowest&nbsp;q&nbsp;vector.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;"No"&nbsp;:&nbsp;q$_0$&nbsp;is&nbsp;zero&nbsp;and&nbsp;mixing&nbsp;is&nbsp;linear&nbsp;(default).<br>
&nbsp;<br>
&nbsp;&nbsp;updatecharge&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;'Yes'&nbsp;or&nbsp;'No'<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;"Yes"&nbsp;:&nbsp;Perform&nbsp;charge&nbsp;mixing&nbsp;according&nbsp;to<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ChargeMixing:Method&nbsp;setting<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;"No"&nbsp;:&nbsp;Freeze&nbsp;charge&nbsp;to&nbsp;initial&nbsp;value.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This&nbsp;setting&nbsp;is&nbsp;useful&nbsp;when&nbsp;evaluating&nbsp;the&nbsp;Harris-Foulkes<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;density&nbsp;functional</tt></dd></dl>

<dl><dt><a name="Jacapo-set_convergence"><strong>set_convergence</strong></a>(self, energy<font color="#909090">=1e-05</font>, density<font color="#909090">=0.0001</font>, occupation<font color="#909090">=0.001</font>, maxsteps<font color="#909090">=None</font>, maxtime<font color="#909090">=None</font>)</dt><dd><tt>set&nbsp;convergence&nbsp;criteria&nbsp;for&nbsp;stopping&nbsp;the&nbsp;dacapo&nbsp;calculator.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;energy&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;set&nbsp;total&nbsp;energy&nbsp;change&nbsp;(eV)&nbsp;required&nbsp;for&nbsp;stopping<br>
&nbsp;<br>
&nbsp;&nbsp;density&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;set&nbsp;density&nbsp;change&nbsp;required&nbsp;for&nbsp;stopping<br>
&nbsp;<br>
&nbsp;&nbsp;occupation&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;set&nbsp;occupation&nbsp;change&nbsp;required&nbsp;for&nbsp;stopping<br>
&nbsp;<br>
&nbsp;&nbsp;maxsteps&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;specify&nbsp;maximum&nbsp;number&nbsp;of&nbsp;steps&nbsp;to&nbsp;take<br>
&nbsp;<br>
&nbsp;&nbsp;maxtime&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;specify&nbsp;maximum&nbsp;number&nbsp;of&nbsp;hours&nbsp;to&nbsp;run.<br>
&nbsp;<br>
Autopilot&nbsp;not&nbsp;supported&nbsp;here.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_debug"><strong>set_debug</strong></a>(self, debug)</dt><dd><tt>set&nbsp;debug&nbsp;level&nbsp;for&nbsp;python&nbsp;logging<br>
&nbsp;<br>
debug&nbsp;should&nbsp;be&nbsp;an&nbsp;integer&nbsp;from&nbsp;0-100&nbsp;or&nbsp;one&nbsp;of&nbsp;the&nbsp;logging<br>
constants&nbsp;like&nbsp;logging.DEBUG,&nbsp;logging.WARN,&nbsp;etc...</tt></dd></dl>

<dl><dt><a name="Jacapo-set_decoupling"><strong>set_decoupling</strong></a>(self, ngaussians<font color="#909090">=3</font>, ecutoff<font color="#909090">=100</font>, gausswidth<font color="#909090">=0.35</font>)</dt><dd><tt>Decoupling&nbsp;activates&nbsp;the&nbsp;three&nbsp;dimensional&nbsp;electrostatic<br>
decoupling.&nbsp;Based&nbsp;on&nbsp;paper&nbsp;by&nbsp;Peter&nbsp;E.&nbsp;Bloechl:&nbsp;JCP&nbsp;103<br>
page7422&nbsp;(1995).<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;ngaussians&nbsp;:&nbsp;int<br>
&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;gaussian&nbsp;functions&nbsp;per&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;used&nbsp;for&nbsp;constructing&nbsp;the&nbsp;model&nbsp;charge&nbsp;of&nbsp;the&nbsp;system<br>
&nbsp;<br>
&nbsp;&nbsp;ecutoff&nbsp;:&nbsp;int<br>
&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;cut&nbsp;off&nbsp;energy&nbsp;(eV)&nbsp;of&nbsp;system&nbsp;charge&nbsp;density&nbsp;in<br>
&nbsp;&nbsp;&nbsp;&nbsp;g-space&nbsp;used&nbsp;when&nbsp;mapping&nbsp;constructing&nbsp;the&nbsp;model&nbsp;change&nbsp;of<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;system,&nbsp;i.e.&nbsp;only&nbsp;charge&nbsp;density&nbsp;components&nbsp;below<br>
&nbsp;&nbsp;&nbsp;&nbsp;ECutoff&nbsp;enters&nbsp;when&nbsp;constructing&nbsp;the&nbsp;model&nbsp;change.<br>
&nbsp;<br>
&nbsp;&nbsp;gausswidth&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;width&nbsp;of&nbsp;the&nbsp;Gaussians&nbsp;defined&nbsp;by<br>
&nbsp;&nbsp;&nbsp;&nbsp;$widthofgaussian*1.5^(n-1)$&nbsp;&nbsp;$n$=(1&nbsp;to&nbsp;numberofgaussians)</tt></dd></dl>

<dl><dt><a name="Jacapo-set_dipole"><strong>set_dipole</strong></a>(self, status<font color="#909090">=True</font>, mixpar<font color="#909090">=0.2</font>, initval<font color="#909090">=0.0</font>, adddipfield<font color="#909090">=0.0</font>, position<font color="#909090">=None</font>)</dt><dd><tt>turn&nbsp;on&nbsp;and&nbsp;set&nbsp;dipole&nbsp;correction&nbsp;scheme<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;status&nbsp;:&nbsp;Boolean<br>
&nbsp;&nbsp;&nbsp;&nbsp;True&nbsp;turns&nbsp;dipole&nbsp;on.&nbsp;False&nbsp;turns&nbsp;Dipole&nbsp;off<br>
&nbsp;<br>
&nbsp;&nbsp;mixpar&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;Mixing&nbsp;Parameter&nbsp;for&nbsp;the&nbsp;the&nbsp;dipole&nbsp;correction&nbsp;field<br>
&nbsp;&nbsp;&nbsp;&nbsp;during&nbsp;the&nbsp;electronic&nbsp;minimization&nbsp;process.&nbsp;If&nbsp;instabilities<br>
&nbsp;&nbsp;&nbsp;&nbsp;occur&nbsp;during&nbsp;electronic&nbsp;minimization,&nbsp;this&nbsp;value&nbsp;may&nbsp;be<br>
&nbsp;&nbsp;&nbsp;&nbsp;decreased.<br>
&nbsp;<br>
&nbsp;&nbsp;initval&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;initial&nbsp;value&nbsp;to&nbsp;start&nbsp;at<br>
&nbsp;<br>
&nbsp;&nbsp;adddipfield&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;additional&nbsp;dipole&nbsp;field&nbsp;to&nbsp;add<br>
&nbsp;&nbsp;&nbsp;&nbsp;units&nbsp;:&nbsp;V/ang<br>
&nbsp;&nbsp;&nbsp;&nbsp;External&nbsp;additive,&nbsp;constant&nbsp;electrostatic&nbsp;field&nbsp;along<br>
&nbsp;&nbsp;&nbsp;&nbsp;third&nbsp;unit&nbsp;cell&nbsp;vector,&nbsp;corresponding&nbsp;to&nbsp;an&nbsp;external<br>
&nbsp;&nbsp;&nbsp;&nbsp;dipole&nbsp;layer.&nbsp;The&nbsp;field&nbsp;discontinuity&nbsp;follows&nbsp;the&nbsp;position<br>
&nbsp;&nbsp;&nbsp;&nbsp;of&nbsp;the&nbsp;dynamical&nbsp;dipole&nbsp;correction,&nbsp;i.e.&nbsp;if<br>
&nbsp;&nbsp;&nbsp;&nbsp;DipoleCorrection:DipoleLayerPosition&nbsp;is&nbsp;set,&nbsp;the&nbsp;field<br>
&nbsp;&nbsp;&nbsp;&nbsp;discontinuity&nbsp;is&nbsp;at&nbsp;this&nbsp;value,&nbsp;otherwise&nbsp;it&nbsp;is&nbsp;at&nbsp;the<br>
&nbsp;&nbsp;&nbsp;&nbsp;vacuum&nbsp;position&nbsp;farthest&nbsp;from&nbsp;any&nbsp;other&nbsp;atoms&nbsp;on&nbsp;both<br>
&nbsp;&nbsp;&nbsp;&nbsp;sides&nbsp;of&nbsp;the&nbsp;slab.<br>
&nbsp;<br>
&nbsp;&nbsp;position&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;scaled&nbsp;coordinates&nbsp;along&nbsp;third&nbsp;unit&nbsp;cell&nbsp;direction.<br>
&nbsp;&nbsp;&nbsp;&nbsp;If&nbsp;this&nbsp;attribute&nbsp;is&nbsp;set,&nbsp;DACAPO&nbsp;will&nbsp;position&nbsp;the<br>
&nbsp;&nbsp;&nbsp;&nbsp;compensation&nbsp;dipole&nbsp;layer&nbsp;plane&nbsp;in&nbsp;at&nbsp;the&nbsp;provided&nbsp;value.<br>
&nbsp;&nbsp;&nbsp;&nbsp;If&nbsp;this&nbsp;attribute&nbsp;is&nbsp;not&nbsp;set,&nbsp;DACAPO&nbsp;will&nbsp;put&nbsp;the&nbsp;compensation<br>
&nbsp;&nbsp;&nbsp;&nbsp;dipole&nbsp;layer&nbsp;plane&nbsp;in&nbsp;the&nbsp;vacuum&nbsp;position&nbsp;farthest&nbsp;from&nbsp;any<br>
&nbsp;&nbsp;&nbsp;&nbsp;other&nbsp;atoms&nbsp;on&nbsp;both&nbsp;sides&nbsp;of&nbsp;the&nbsp;slab.&nbsp;Do&nbsp;not&nbsp;set&nbsp;this&nbsp;to<br>
&nbsp;&nbsp;&nbsp;&nbsp;0.0<br>
&nbsp;<br>
&nbsp;<br>
calling&nbsp;<a href="#Jacapo-set_dipole">set_dipole</a>()&nbsp;sets&nbsp;all&nbsp;default&nbsp;values.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_dw"><strong>set_dw</strong></a>(self, dw)</dt><dd><tt>set&nbsp;the&nbsp;density&nbsp;wave&nbsp;cutoff&nbsp;energy.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;dw&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;density&nbsp;wave&nbsp;cutoff<br>
&nbsp;<br>
The&nbsp;function&nbsp;checks&nbsp;to&nbsp;make&nbsp;sure&nbsp;it&nbsp;is&nbsp;not&nbsp;less&nbsp;than&nbsp;the<br>
planewave&nbsp;cutoff.<br>
&nbsp;<br>
Density_WaveCutoff&nbsp;describes&nbsp;the&nbsp;kinetic&nbsp;energy&nbsp;neccesary&nbsp;to<br>
represent&nbsp;a&nbsp;wavefunction&nbsp;associated&nbsp;with&nbsp;the&nbsp;total&nbsp;density,<br>
i.e.&nbsp;G-vectors&nbsp;for&nbsp;which&nbsp;$ert&nbsp;Gert^2$&nbsp;$&lt;$<br>
4*Density_WaveCutoff&nbsp;will&nbsp;be&nbsp;used&nbsp;to&nbsp;describe&nbsp;the&nbsp;total<br>
density&nbsp;(including&nbsp;augmentation&nbsp;charge&nbsp;and&nbsp;partial&nbsp;core<br>
density).&nbsp;If&nbsp;Density_WaveCutoff&nbsp;is&nbsp;equal&nbsp;to&nbsp;PlaneWaveCutoff<br>
this&nbsp;implies&nbsp;that&nbsp;the&nbsp;total&nbsp;density&nbsp;is&nbsp;as&nbsp;soft&nbsp;as&nbsp;the<br>
wavefunctions&nbsp;described&nbsp;by&nbsp;the&nbsp;kinetic&nbsp;energy&nbsp;cutoff<br>
PlaneWaveCutoff.&nbsp;If&nbsp;a&nbsp;value&nbsp;of&nbsp;Density_WaveCutoff&nbsp;is&nbsp;specified<br>
(must&nbsp;be&nbsp;larger&nbsp;than&nbsp;or&nbsp;equal&nbsp;to&nbsp;PlaneWaveCutoff)&nbsp;the&nbsp;program<br>
will&nbsp;run&nbsp;using&nbsp;two&nbsp;grids,&nbsp;one&nbsp;for&nbsp;representing&nbsp;the<br>
wavefunction&nbsp;density&nbsp;(softgrid_dim)&nbsp;and&nbsp;one&nbsp;representing&nbsp;the<br>
total&nbsp;density&nbsp;(hardgrid_dim).&nbsp;If&nbsp;the&nbsp;density&nbsp;can&nbsp;be<br>
reprensented&nbsp;on&nbsp;the&nbsp;same&nbsp;grid&nbsp;as&nbsp;the&nbsp;wavefunction&nbsp;density<br>
Density_WaveCutoff&nbsp;can&nbsp;be&nbsp;chosen&nbsp;equal&nbsp;to&nbsp;PlaneWaveCutoff<br>
(default).</tt></dd></dl>

<dl><dt><a name="Jacapo-set_electronic_minimization"><strong>set_electronic_minimization</strong></a>(self, method<font color="#909090">='eigsolve'</font>, diagsperband<font color="#909090">=2</font>)</dt><dd><tt>set&nbsp;the&nbsp;eigensolver&nbsp;method<br>
&nbsp;<br>
Selector&nbsp;for&nbsp;which&nbsp;subroutine&nbsp;to&nbsp;use&nbsp;for&nbsp;electronic<br>
minimization<br>
&nbsp;<br>
Recognized&nbsp;options&nbsp;:&nbsp;"resmin",&nbsp;"eigsolve"&nbsp;and&nbsp;"rmm-diis".<br>
&nbsp;<br>
*&nbsp;"resmin"&nbsp;:&nbsp;Power&nbsp;method&nbsp;(Lennart&nbsp;Bengtson),&nbsp;can&nbsp;only&nbsp;handle<br>
&nbsp;&nbsp;&nbsp;k-point&nbsp;parallization.<br>
&nbsp;<br>
*&nbsp;"eigsolve&nbsp;:&nbsp;Block&nbsp;Davidson&nbsp;algorithm<br>
&nbsp;&nbsp;&nbsp;(Claus&nbsp;Bendtsen&nbsp;et&nbsp;al).<br>
&nbsp;<br>
*&nbsp;"rmm-diis&nbsp;:&nbsp;Residual&nbsp;minimization<br>
&nbsp;&nbsp;&nbsp;method&nbsp;(RMM),&nbsp;using&nbsp;DIIS&nbsp;(direct&nbsp;inversion&nbsp;in&nbsp;the&nbsp;iterate<br>
&nbsp;&nbsp;&nbsp;subspace)&nbsp;The&nbsp;implementaion&nbsp;follows&nbsp;closely&nbsp;the&nbsp;algorithm<br>
&nbsp;&nbsp;&nbsp;outlined&nbsp;in&nbsp;Kresse&nbsp;and&nbsp;Furthmuller,&nbsp;Comp.&nbsp;Mat.&nbsp;Sci,&nbsp;III.G/III.H<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;method&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;should&nbsp;be&nbsp;'resmin',&nbsp;'eigsolve'&nbsp;or&nbsp;'rmm-diis'<br>
&nbsp;<br>
&nbsp;&nbsp;diagsperband&nbsp;:&nbsp;int<br>
&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;diagonalizations&nbsp;per&nbsp;band&nbsp;for<br>
&nbsp;&nbsp;&nbsp;&nbsp;electronic&nbsp;minimization&nbsp;algorithms&nbsp;(maps&nbsp;onto&nbsp;internal<br>
&nbsp;&nbsp;&nbsp;&nbsp;variable&nbsp;ndiapb).&nbsp;Applies&nbsp;for&nbsp;both<br>
&nbsp;&nbsp;&nbsp;&nbsp;ElectronicMinimization:Method&nbsp;=&nbsp;"resmin"&nbsp;and&nbsp;"eigsolve".<br>
&nbsp;&nbsp;&nbsp;&nbsp;default&nbsp;value&nbsp;=&nbsp;2</tt></dd></dl>

<dl><dt><a name="Jacapo-set_external_dipole"><strong>set_external_dipole</strong></a>(self, value, position<font color="#909090">=None</font>)</dt><dd><tt>Externally&nbsp;imposed&nbsp;dipole&nbsp;potential.&nbsp;This&nbsp;option&nbsp;overwrites<br>
DipoleCorrection&nbsp;if&nbsp;set.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;value&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;units&nbsp;of&nbsp;volts<br>
&nbsp;<br>
&nbsp;&nbsp;position&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;scaled&nbsp;coordinates&nbsp;along&nbsp;third&nbsp;unit&nbsp;cell&nbsp;direction.<br>
&nbsp;&nbsp;&nbsp;&nbsp;if&nbsp;None,&nbsp;the&nbsp;compensation&nbsp;dipole&nbsp;layer&nbsp;plane&nbsp;in&nbsp;the<br>
&nbsp;&nbsp;&nbsp;&nbsp;vacuum&nbsp;position&nbsp;farthest&nbsp;from&nbsp;any&nbsp;other&nbsp;atoms&nbsp;on&nbsp;both<br>
&nbsp;&nbsp;&nbsp;&nbsp;sides&nbsp;of&nbsp;the&nbsp;slab.&nbsp;Do&nbsp;not&nbsp;set&nbsp;to&nbsp;0.0.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_extpot"><strong>set_extpot</strong></a>(self, potgrid)</dt><dd><tt>add&nbsp;external&nbsp;potential&nbsp;of&nbsp;value<br>
&nbsp;<br>
see&nbsp;this&nbsp;link&nbsp;before&nbsp;using&nbsp;this<br>
https://listserv.fysik.dtu.dk/pipermail/campos/2003-August/000657.html<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;potgrid&nbsp;:&nbsp;np.array&nbsp;with&nbsp;shape&nbsp;(nx,ny,nz)<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;shape&nbsp;must&nbsp;be&nbsp;the&nbsp;same&nbsp;as&nbsp;the&nbsp;fft&nbsp;soft&nbsp;grid<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;value&nbsp;of&nbsp;the&nbsp;potential&nbsp;to&nbsp;add<br>
&nbsp;<br>
&nbsp;<br>
you&nbsp;have&nbsp;to&nbsp;know&nbsp;both&nbsp;of&nbsp;the&nbsp;fft&nbsp;grid&nbsp;dimensions&nbsp;ahead&nbsp;of&nbsp;time!<br>
if&nbsp;you&nbsp;know&nbsp;what&nbsp;you&nbsp;are&nbsp;doing,&nbsp;you&nbsp;can&nbsp;set&nbsp;the&nbsp;fft_grid&nbsp;you&nbsp;want<br>
before&nbsp;hand&nbsp;with:<br>
calc.<a href="#Jacapo-set_fftgrid">set_fftgrid</a>((n1,n2,n3))</tt></dd></dl>

<dl><dt><a name="Jacapo-set_extracharge"><strong>set_extracharge</strong></a>(self, val)</dt><dd><tt>add&nbsp;extra&nbsp;charge&nbsp;to&nbsp;unit&nbsp;cell<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;val&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;extra&nbsp;electrons&nbsp;to&nbsp;add&nbsp;or&nbsp;subtract&nbsp;from&nbsp;the&nbsp;unit&nbsp;cell<br>
&nbsp;<br>
Fixed&nbsp;extra&nbsp;charge&nbsp;in&nbsp;the&nbsp;unit&nbsp;cell&nbsp;(i.e.&nbsp;deviation&nbsp;from<br>
charge&nbsp;neutrality).&nbsp;This&nbsp;assumes&nbsp;a&nbsp;compensating,&nbsp;positive<br>
constant&nbsp;backgound&nbsp;charge&nbsp;(jellium)&nbsp;to&nbsp;forge&nbsp;overall&nbsp;charge<br>
neutrality.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_fftgrid"><strong>set_fftgrid</strong></a>(self, soft<font color="#909090">=None</font>, hard<font color="#909090">=None</font>)</dt><dd><tt>sets&nbsp;the&nbsp;dimensions&nbsp;of&nbsp;the&nbsp;FFT&nbsp;grid&nbsp;to&nbsp;be&nbsp;used<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;soft&nbsp;:&nbsp;(n1,n2,n3)&nbsp;integers<br>
&nbsp;&nbsp;&nbsp;&nbsp;make&nbsp;a&nbsp;n1&nbsp;x&nbsp;n2&nbsp;x&nbsp;n3&nbsp;grid<br>
&nbsp;<br>
&nbsp;&nbsp;hard&nbsp;:&nbsp;(n1,n2,n3)&nbsp;integers<br>
&nbsp;&nbsp;&nbsp;&nbsp;make&nbsp;a&nbsp;n1&nbsp;x&nbsp;n2&nbsp;x&nbsp;n3&nbsp;grid<br>
&nbsp;<br>
&nbsp;<br>
&gt;&gt;&gt;&nbsp;calc.<a href="#Jacapo-set_fftgrid">set_fftgrid</a>(soft=[42,44,46])<br>
sets&nbsp;the&nbsp;soft&nbsp;and&nbsp;hard&nbsp;grid&nbsp;dimensions&nbsp;to&nbsp;42,44,46<br>
&nbsp;<br>
&gt;&gt;&gt;&nbsp;calc.<a href="#Jacapo-set_fftgrid">set_fftgrid</a>(soft=[42,44,46],hard=[80,84,88])<br>
sets&nbsp;the&nbsp;soft&nbsp;grid&nbsp;dimensions&nbsp;to&nbsp;42,44,46&nbsp;and&nbsp;the&nbsp;hard<br>
grid&nbsp;dimensions&nbsp;to&nbsp;80,84,88<br>
&nbsp;<br>
These&nbsp;are&nbsp;the&nbsp;fast&nbsp;FFt&nbsp;grid&nbsp;numbers&nbsp;listed&nbsp;in&nbsp;fftdimensions.F<br>
&nbsp;<br>
data&nbsp;list_of_fft&nbsp;/2,&nbsp;&nbsp;4,&nbsp;&nbsp;6,&nbsp;&nbsp;8,&nbsp;10,&nbsp;12,&nbsp;14,&nbsp;16,&nbsp;18,&nbsp;20,&nbsp;&amp;<br>
22,24,&nbsp;28,&nbsp;30,32,&nbsp;36,&nbsp;40,&nbsp;42,&nbsp;44,&nbsp;48,&nbsp;&amp;<br>
56,60,&nbsp;64,&nbsp;66,&nbsp;70,&nbsp;72,&nbsp;80,&nbsp;84,&nbsp;88,&nbsp;90,&nbsp;&amp;<br>
96,108,110,112,120,126,128,132,140,144,154,&nbsp;&amp;<br>
160,168,176,180,192,198,200,&nbsp;&amp;<br>
216,240,264,270,280,288,324,352,360,378,384,400,432,&nbsp;&amp;<br>
450,480,540,576,640/<br>
&nbsp;<br>
otherwise&nbsp;you&nbsp;will&nbsp;get&nbsp;some&nbsp;errors&nbsp;from&nbsp;mis-dimensioned&nbsp;variables.<br>
&nbsp;<br>
this&nbsp;is&nbsp;usually&nbsp;automatically&nbsp;set&nbsp;by&nbsp;Dacapo.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_fixmagmom"><strong>set_fixmagmom</strong></a>(self, fixmagmom<font color="#909090">=None</font>)</dt><dd><tt>set&nbsp;a&nbsp;fixed&nbsp;magnetic&nbsp;moment&nbsp;for&nbsp;a&nbsp;spin&nbsp;polarized&nbsp;calculation<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;fixmagmom&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;magnetic&nbsp;moment&nbsp;of&nbsp;the&nbsp;cell&nbsp;in&nbsp;Bohr&nbsp;magnetons</tt></dd></dl>

<dl><dt><a name="Jacapo-set_ft"><strong>set_ft</strong></a>(self, ft)</dt><dd><tt>set&nbsp;the&nbsp;Fermi&nbsp;temperature&nbsp;for&nbsp;occupation&nbsp;smearing<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;ft&nbsp;:&nbsp;float<br>
&nbsp;&nbsp;&nbsp;&nbsp;Fermi&nbsp;temperature&nbsp;in&nbsp;kT&nbsp;(eV)<br>
&nbsp;<br>
Electronic&nbsp;temperature,&nbsp;corresponding&nbsp;to&nbsp;gaussian&nbsp;occupation<br>
statistics.&nbsp;Device&nbsp;used&nbsp;to&nbsp;stabilize&nbsp;the&nbsp;convergence&nbsp;towards<br>
the&nbsp;electronic&nbsp;ground&nbsp;state.&nbsp;Higher&nbsp;values&nbsp;stabilizes&nbsp;the<br>
convergence.&nbsp;Values&nbsp;in&nbsp;the&nbsp;range&nbsp;0.1-1.0&nbsp;eV&nbsp;are&nbsp;recommended,<br>
depending&nbsp;on&nbsp;the&nbsp;complexity&nbsp;of&nbsp;the&nbsp;Fermi&nbsp;surface&nbsp;(low&nbsp;values<br>
for&nbsp;d-metals&nbsp;and&nbsp;narrow&nbsp;gap&nbsp;semiconducters,&nbsp;higher&nbsp;for&nbsp;free<br>
electron-like&nbsp;metals).</tt></dd></dl>

<dl><dt><a name="Jacapo-set_kpts"><strong>set_kpts</strong></a>(self, kpts)</dt><dd><tt>set&nbsp;the&nbsp;kpt&nbsp;grid.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;<br>
kpts:&nbsp;(n1,n2,n3)&nbsp;or&nbsp;[k1,k2,k3,...]&nbsp;or&nbsp;one&nbsp;of&nbsp;these<br>
chadi-cohen&nbsp;sets:<br>
&nbsp;<br>
*&nbsp;cc6_1x1<br>
*&nbsp;cc12_2x3<br>
*&nbsp;cc18_sq3xsq3<br>
*&nbsp;cc18_1x1<br>
*&nbsp;cc54_sq3xsq3<br>
*&nbsp;cc54_1x1<br>
*&nbsp;cc162_sq3xsq3<br>
*&nbsp;cc162_1x1<br>
&nbsp;<br>
(n1,n2,n3)&nbsp;creates&nbsp;an&nbsp;n1&nbsp;x&nbsp;n2&nbsp;x&nbsp;n3&nbsp;monkhorst-pack&nbsp;grid,<br>
[k1,k2,k3,...]&nbsp;creates&nbsp;a&nbsp;kpt-grid&nbsp;based&nbsp;on&nbsp;the&nbsp;kpoints<br>
defined&nbsp;in&nbsp;k1,k2,k3,...<br>
&nbsp;<br>
There&nbsp;is&nbsp;also&nbsp;a&nbsp;possibility&nbsp;to&nbsp;have&nbsp;Dacapo&nbsp;(fortran)&nbsp;create<br>
the&nbsp;Kpoints&nbsp;in&nbsp;chadi-cohen&nbsp;or&nbsp;monkhorst-pack&nbsp;form.&nbsp;To&nbsp;do&nbsp;this<br>
you&nbsp;need&nbsp;to&nbsp;set&nbsp;the&nbsp;KpointSetup.gridtype&nbsp;attribute,&nbsp;and<br>
KpointSetup.<br>
&nbsp;<br>
KpointSetup&nbsp;=&nbsp;[3,0,0]<br>
KpointSetup.gridtype&nbsp;=&nbsp;'ChadiCohen'<br>
&nbsp;<br>
KpointSetup(1)&nbsp;&nbsp;Chadi-Cohen&nbsp;k-point&nbsp;set<br>
1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;6&nbsp;k-points&nbsp;1x1<br>
2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;18-kpoints&nbsp;sqrt(3)*sqrt(3)<br>
3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;18-kpoints&nbsp;1x1<br>
4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;54-kpoints&nbsp;sqrt(3)*sqrt(3)<br>
5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;54-kpoints&nbsp;1x1<br>
6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;162-kpoints&nbsp;1x1<br>
7&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;12-kpoints&nbsp;2x3<br>
8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;162-kpoints&nbsp;3xsqrt&nbsp;3<br>
&nbsp;<br>
or<br>
KpointSetup&nbsp;=&nbsp;[4,4,4]<br>
KpointSetup.gridtype&nbsp;=&nbsp;'MonkhorstPack'<br>
we&nbsp;do&nbsp;not&nbsp;use&nbsp;this&nbsp;functionality.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_mdos"><strong>set_mdos</strong></a>(self, mcenters<font color="#909090">=None</font>, energywindow<font color="#909090">=(-15, 5)</font>, energywidth<font color="#909090">=0.2</font>, numberenergypoints<font color="#909090">=250</font>, cutoffradius<font color="#909090">=1.0</font>)</dt><dd><tt>Setup&nbsp;multicentered&nbsp;projected&nbsp;DOS.<br>
&nbsp;<br>
mcenters<br>
&nbsp;&nbsp;&nbsp;a&nbsp;list&nbsp;of&nbsp;tuples&nbsp;containing&nbsp;(atom#,l,m,weight)<br>
&nbsp;&nbsp;&nbsp;(0,0,0,1.0)&nbsp;specifies&nbsp;(atom&nbsp;0,&nbsp;l=0,&nbsp;m=0,&nbsp;weight=1.0)&nbsp;an&nbsp;s&nbsp;orbital<br>
&nbsp;&nbsp;&nbsp;on&nbsp;atom&nbsp;0<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;(1,1,1,1.0)&nbsp;specifies&nbsp;(atom&nbsp;1,&nbsp;l=1,&nbsp;m=1,&nbsp;weight=1.0)&nbsp;a&nbsp;p&nbsp;orbital<br>
&nbsp;&nbsp;&nbsp;with&nbsp;m&nbsp;=&nbsp;+1&nbsp;on&nbsp;atom&nbsp;0<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;l=0&nbsp;s-orbital<br>
&nbsp;&nbsp;&nbsp;l=1&nbsp;p-orbital<br>
&nbsp;&nbsp;&nbsp;l=2&nbsp;d-orbital<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;m&nbsp;in&nbsp;range&nbsp;of&nbsp;(&nbsp;-l&nbsp;...&nbsp;0&nbsp;...&nbsp;+l&nbsp;)<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;The&nbsp;direction&nbsp;cosines&nbsp;for&nbsp;which&nbsp;the&nbsp;spherical&nbsp;harmonics&nbsp;are<br>
&nbsp;&nbsp;&nbsp;set&nbsp;up&nbsp;are&nbsp;using&nbsp;the&nbsp;next&nbsp;different&nbsp;atom&nbsp;in&nbsp;the&nbsp;list<br>
&nbsp;&nbsp;&nbsp;(cyclic)&nbsp;as&nbsp;direction&nbsp;pointer,&nbsp;so&nbsp;the&nbsp;z-direction&nbsp;is&nbsp;chosen<br>
&nbsp;&nbsp;&nbsp;along&nbsp;the&nbsp;direction&nbsp;to&nbsp;this&nbsp;next&nbsp;atom.&nbsp;At&nbsp;the&nbsp;moment&nbsp;the<br>
&nbsp;&nbsp;&nbsp;rotation&nbsp;matrices&nbsp;is&nbsp;only&nbsp;given&nbsp;in&nbsp;the&nbsp;text&nbsp;file,&nbsp;you&nbsp;can<br>
&nbsp;&nbsp;&nbsp;use&nbsp;grep'MUL:&nbsp;Rmatrix'&nbsp;out_o2.txt&nbsp;to&nbsp;get&nbsp;this&nbsp;information.<br>
&nbsp;<br>
adapated&nbsp;from&nbsp;old&nbsp;MultiCenterProjectedDOS.py</tt></dd></dl>

<dl><dt><a name="Jacapo-set_nbands"><strong>set_nbands</strong></a>(self, nbands<font color="#909090">=None</font>)</dt><dd><tt>Set&nbsp;the&nbsp;number&nbsp;of&nbsp;bands.&nbsp;a&nbsp;few&nbsp;unoccupied&nbsp;bands&nbsp;are<br>
recommended.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;nbands&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;number&nbsp;of&nbsp;bands.<br>
&nbsp;<br>
if&nbsp;nbands&nbsp;=&nbsp;None&nbsp;the&nbsp;function&nbsp;returns&nbsp;with&nbsp;nothing&nbsp;done.&nbsp;At<br>
calculate&nbsp;time,&nbsp;if&nbsp;there&nbsp;are&nbsp;still&nbsp;no&nbsp;bands,&nbsp;they&nbsp;will&nbsp;be&nbsp;set<br>
by:<br>
&nbsp;<br>
the&nbsp;number&nbsp;of&nbsp;bands&nbsp;is&nbsp;calculated&nbsp;as<br>
$nbands=nvalence*0.65&nbsp;+&nbsp;4$</tt></dd></dl>

<dl><dt><a name="Jacapo-set_nc"><strong>set_nc</strong></a>(self, nc<font color="#909090">='out.nc'</font>)</dt><dd><tt>set&nbsp;filename&nbsp;for&nbsp;the&nbsp;netcdf&nbsp;and&nbsp;text&nbsp;output&nbsp;for&nbsp;this&nbsp;calculation<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;nc&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;filename&nbsp;for&nbsp;netcdf&nbsp;file<br>
&nbsp;<br>
if&nbsp;the&nbsp;ncfile&nbsp;attached&nbsp;to&nbsp;the&nbsp;calculator&nbsp;is&nbsp;changing,&nbsp;the&nbsp;old<br>
file&nbsp;will&nbsp;be&nbsp;copied&nbsp;to&nbsp;the&nbsp;new&nbsp;file&nbsp;if&nbsp;it&nbsp;doesn&nbsp;not&nbsp;exist&nbsp;so<br>
that&nbsp;all&nbsp;the&nbsp;calculator&nbsp;details&nbsp;are&nbsp;preserved.&nbsp;Otherwise,&nbsp;the<br>
&nbsp;<br>
if&nbsp;the&nbsp;ncfile&nbsp;does&nbsp;not&nbsp;exist,&nbsp;it&nbsp;will&nbsp;get&nbsp;initialized.<br>
&nbsp;<br>
the&nbsp;text&nbsp;file&nbsp;will&nbsp;have&nbsp;the&nbsp;same&nbsp;basename&nbsp;as&nbsp;the&nbsp;ncfile,&nbsp;but<br>
with&nbsp;a&nbsp;.txt&nbsp;extension.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_ncoutput"><strong>set_ncoutput</strong></a>(self, wf<font color="#909090">=None</font>, cd<font color="#909090">=None</font>, efp<font color="#909090">=None</font>, esp<font color="#909090">=None</font>)</dt><dd><tt>set&nbsp;the&nbsp;output&nbsp;of&nbsp;large&nbsp;variables&nbsp;in&nbsp;the&nbsp;netcdf&nbsp;output&nbsp;file<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;wf&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;controls&nbsp;output&nbsp;of&nbsp;wavefunction.&nbsp;values&nbsp;can<br>
&nbsp;&nbsp;&nbsp;&nbsp;be&nbsp;'Yes'&nbsp;or&nbsp;'No'<br>
&nbsp;<br>
&nbsp;&nbsp;cd&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;controls&nbsp;output&nbsp;of&nbsp;charge&nbsp;density.&nbsp;values&nbsp;can<br>
&nbsp;&nbsp;&nbsp;&nbsp;be&nbsp;'Yes'&nbsp;or&nbsp;'No'<br>
&nbsp;<br>
&nbsp;&nbsp;efp&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;controls&nbsp;output&nbsp;of&nbsp;effective&nbsp;potential.&nbsp;values&nbsp;can<br>
&nbsp;&nbsp;&nbsp;&nbsp;be&nbsp;'Yes'&nbsp;or&nbsp;'No'<br>
&nbsp;<br>
&nbsp;&nbsp;esp&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;controls&nbsp;output&nbsp;of&nbsp;electrostatic&nbsp;potential.&nbsp;values&nbsp;can<br>
&nbsp;&nbsp;&nbsp;&nbsp;be&nbsp;'Yes'&nbsp;or&nbsp;'No'</tt></dd></dl>

<dl><dt><a name="Jacapo-set_occupationstatistics"><strong>set_occupationstatistics</strong></a>(self, method)</dt><dd><tt>set&nbsp;the&nbsp;method&nbsp;used&nbsp;for&nbsp;smearing&nbsp;the&nbsp;occupations.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;method&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;one&nbsp;of&nbsp;'FermiDirac'&nbsp;or&nbsp;'MethfesselPaxton'<br>
&nbsp;&nbsp;&nbsp;&nbsp;Currently,&nbsp;the&nbsp;Methfessel-Paxton&nbsp;scheme&nbsp;(PRB&nbsp;40,&nbsp;3616&nbsp;(1989).)<br>
&nbsp;&nbsp;&nbsp;&nbsp;is&nbsp;implemented&nbsp;to&nbsp;1th&nbsp;order&nbsp;(which&nbsp;is&nbsp;recommemded&nbsp;by&nbsp;most&nbsp;authors).<br>
&nbsp;&nbsp;&nbsp;&nbsp;'FermiDirac'&nbsp;is&nbsp;the&nbsp;default</tt></dd></dl>

<dl><dt><a name="Jacapo-set_parent"><strong>set_parent</strong></a>(self, parent)</dt></dl>

<dl><dt><a name="Jacapo-set_pseudopotentials"><strong>set_pseudopotentials</strong></a>(self, pspdict)</dt><dd><tt>Set&nbsp;all&nbsp;the&nbsp;pseudopotentials&nbsp;from&nbsp;a&nbsp;dictionary.<br>
&nbsp;<br>
The&nbsp;dictionary&nbsp;should&nbsp;have&nbsp;this&nbsp;form::<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;{symbol1:&nbsp;path1,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;symbol2:&nbsp;path2}</tt></dd></dl>

<dl><dt><a name="Jacapo-set_psp"><strong>set_psp</strong></a>(self, sym<font color="#909090">=None</font>, z<font color="#909090">=None</font>, psp<font color="#909090">=None</font>)</dt><dd><tt>set&nbsp;the&nbsp;pseudopotential&nbsp;file&nbsp;for&nbsp;a&nbsp;species&nbsp;or&nbsp;an&nbsp;atomic&nbsp;number.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;sym&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;chemical&nbsp;symbol&nbsp;of&nbsp;the&nbsp;species<br>
&nbsp;<br>
&nbsp;&nbsp;z&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;atomic&nbsp;number&nbsp;of&nbsp;the&nbsp;species<br>
&nbsp;<br>
&nbsp;&nbsp;psp&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;filename&nbsp;of&nbsp;the&nbsp;pseudopotential<br>
&nbsp;<br>
&nbsp;<br>
you&nbsp;can&nbsp;only&nbsp;set&nbsp;sym&nbsp;or&nbsp;z.<br>
&nbsp;<br>
examples::<br>
&nbsp;<br>
&nbsp;&nbsp;<a href="#Jacapo-set_psp">set_psp</a>('N',psp='pspfile')<br>
&nbsp;&nbsp;<a href="#Jacapo-set_psp">set_psp</a>(z=6,psp='pspfile')</tt></dd></dl>

<dl><dt><a name="Jacapo-set_psp_database"><strong>set_psp_database</strong></a>(self, xc<font color="#909090">=None</font>)</dt><dd><tt>get&nbsp;the&nbsp;xc-dependent&nbsp;psp&nbsp;database<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;xc&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;one&nbsp;of&nbsp;'PW91',&nbsp;'PBE',&nbsp;'revPBE',&nbsp;'RPBE',&nbsp;'PZ'<br>
&nbsp;<br>
&nbsp;<br>
not&nbsp;all&nbsp;the&nbsp;databases&nbsp;are&nbsp;complete,&nbsp;and&nbsp;that&nbsp;means<br>
some&nbsp;psp&nbsp;do&nbsp;not&nbsp;exist.<br>
&nbsp;<br>
note:&nbsp;this&nbsp;function&nbsp;is&nbsp;not&nbsp;supported&nbsp;fully.&nbsp;only&nbsp;pw91&nbsp;is<br>
imported&nbsp;now.&nbsp;Changing&nbsp;the&nbsp;xc&nbsp;at&nbsp;this&nbsp;point&nbsp;results&nbsp;in&nbsp;loading<br>
a&nbsp;nearly&nbsp;empty&nbsp;database,&nbsp;and&nbsp;I&nbsp;have&nbsp;not&nbsp;thought&nbsp;about&nbsp;how&nbsp;to<br>
resolve&nbsp;that</tt></dd></dl>

<dl><dt><a name="Jacapo-set_pw"><strong>set_pw</strong></a>(self, pw)</dt><dd><tt>set&nbsp;the&nbsp;planewave&nbsp;cutoff.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;pw&nbsp;:&nbsp;integer<br>
&nbsp;&nbsp;&nbsp;the&nbsp;planewave&nbsp;cutoff&nbsp;in&nbsp;eV<br>
&nbsp;<br>
this&nbsp;function&nbsp;checks&nbsp;to&nbsp;make&nbsp;sure&nbsp;the&nbsp;density&nbsp;wave&nbsp;cutoff&nbsp;is<br>
greater&nbsp;than&nbsp;or&nbsp;equal&nbsp;to&nbsp;the&nbsp;planewave&nbsp;cutoff.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_spinpol"><strong>set_spinpol</strong></a>(self, spinpol<font color="#909090">=False</font>)</dt><dd><tt>set&nbsp;Spin&nbsp;polarization.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;spinpol&nbsp;:&nbsp;Boolean<br>
&nbsp;&nbsp;&nbsp;<a href="#Jacapo-set_spinpol">set_spinpol</a>(True)&nbsp;&nbsp;spin-polarized.<br>
&nbsp;&nbsp;&nbsp;<a href="#Jacapo-set_spinpol">set_spinpol</a>(False)&nbsp;no&nbsp;spin&nbsp;polarization,&nbsp;default<br>
&nbsp;<br>
Specify&nbsp;whether&nbsp;to&nbsp;perform&nbsp;a&nbsp;spin&nbsp;polarized&nbsp;or&nbsp;unpolarized<br>
calculation.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_status"><strong>set_status</strong></a>(self, status)</dt><dd><tt>set&nbsp;the&nbsp;status&nbsp;flag&nbsp;in&nbsp;the&nbsp;netcdf&nbsp;file<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;status&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;status&nbsp;flag,&nbsp;e.g.&nbsp;'new',&nbsp;'finished'</tt></dd></dl>

<dl><dt><a name="Jacapo-set_stay_alive"><strong>set_stay_alive</strong></a>(self, value)</dt><dd><tt>set&nbsp;the&nbsp;stay&nbsp;alive&nbsp;setting</tt></dd></dl>

<dl><dt><a name="Jacapo-set_symmetry"><strong>set_symmetry</strong></a>(self, val<font color="#909090">=False</font>)</dt><dd><tt>set&nbsp;how&nbsp;symmetry&nbsp;is&nbsp;used&nbsp;to&nbsp;reduce&nbsp;k-points<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;val&nbsp;:&nbsp;Boolean<br>
&nbsp;&nbsp;&nbsp;set_sym(True)&nbsp;Maximum&nbsp;symmetry&nbsp;is&nbsp;used<br>
&nbsp;&nbsp;&nbsp;set_sym(False)&nbsp;No&nbsp;symmetry&nbsp;is&nbsp;used<br>
&nbsp;<br>
This&nbsp;variable&nbsp;controls&nbsp;the&nbsp;if&nbsp;and&nbsp;how&nbsp;DACAPO&nbsp;should&nbsp;attempt<br>
using&nbsp;symmetry&nbsp;in&nbsp;the&nbsp;calculation.&nbsp;Imposing&nbsp;symmetry&nbsp;generally<br>
speeds&nbsp;up&nbsp;the&nbsp;calculation&nbsp;and&nbsp;reduces&nbsp;numerical&nbsp;noise&nbsp;to&nbsp;some<br>
extent.&nbsp;Symmetry&nbsp;should&nbsp;always&nbsp;be&nbsp;applied&nbsp;to&nbsp;the&nbsp;maximum<br>
extent,&nbsp;when&nbsp;ions&nbsp;are&nbsp;not&nbsp;moved.&nbsp;When&nbsp;relaxing&nbsp;ions,&nbsp;however,<br>
the&nbsp;symmetry&nbsp;of&nbsp;the&nbsp;equilibrium&nbsp;state&nbsp;may&nbsp;be&nbsp;lower&nbsp;than&nbsp;the<br>
initial&nbsp;state.&nbsp;Such&nbsp;an&nbsp;equilibrium&nbsp;state&nbsp;with&nbsp;lower&nbsp;symmetry<br>
is&nbsp;missed,&nbsp;if&nbsp;symmetry&nbsp;is&nbsp;imposed.&nbsp;Molecular&nbsp;dynamics-like<br>
algorithms&nbsp;for&nbsp;ionic&nbsp;propagation&nbsp;will&nbsp;generally&nbsp;not&nbsp;break&nbsp;the<br>
symmetry&nbsp;of&nbsp;the&nbsp;initial&nbsp;state,&nbsp;but&nbsp;some&nbsp;algorithms,&nbsp;like&nbsp;the<br>
BFGS&nbsp;may&nbsp;break&nbsp;the&nbsp;symmetry&nbsp;of&nbsp;the&nbsp;initial&nbsp;state.&nbsp;Recognized<br>
options:<br>
&nbsp;<br>
"Off":&nbsp;No&nbsp;symmetry&nbsp;will&nbsp;be&nbsp;imposed,&nbsp;apart&nbsp;from&nbsp;time&nbsp;inversion<br>
symmetry&nbsp;in&nbsp;recipical&nbsp;space.&nbsp;This&nbsp;is&nbsp;utilized&nbsp;to&nbsp;reduce&nbsp;the<br>
k-point&nbsp;sampling&nbsp;set&nbsp;for&nbsp;Brillouin&nbsp;zone&nbsp;integration&nbsp;and&nbsp;has&nbsp;no<br>
influence&nbsp;on&nbsp;the&nbsp;ionic&nbsp;forces/motion.<br>
&nbsp;<br>
"Maximum":&nbsp;DACAPO&nbsp;will&nbsp;look&nbsp;for&nbsp;symmetry&nbsp;in&nbsp;the&nbsp;supplied<br>
atomic&nbsp;structure&nbsp;and&nbsp;extract&nbsp;the&nbsp;highest&nbsp;possible&nbsp;symmetry<br>
group.&nbsp;During&nbsp;the&nbsp;calculation,&nbsp;DACAPO&nbsp;will&nbsp;impose&nbsp;the&nbsp;found<br>
spatial&nbsp;symmetry&nbsp;on&nbsp;ionic&nbsp;forces&nbsp;and&nbsp;electronic&nbsp;structure,<br>
i.e.&nbsp;the&nbsp;symmetry&nbsp;will&nbsp;be&nbsp;conserved&nbsp;during&nbsp;the&nbsp;calculation.</tt></dd></dl>

<dl><dt><a name="Jacapo-set_xc"><strong>set_xc</strong></a>(self, xc)</dt><dd><tt>Set&nbsp;the&nbsp;self-consistent&nbsp;exchange-correlation&nbsp;functional<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;xc&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;Must&nbsp;be&nbsp;one&nbsp;of&nbsp;'PZ',&nbsp;'VWN',&nbsp;'PW91',&nbsp;'PBE',&nbsp;'revPBE',&nbsp;'RPBE'<br>
&nbsp;<br>
Selects&nbsp;which&nbsp;density&nbsp;functional&nbsp;to&nbsp;use&nbsp;for<br>
exchange-correlation&nbsp;when&nbsp;performing&nbsp;electronic&nbsp;minimization<br>
(the&nbsp;electronic&nbsp;energy&nbsp;is&nbsp;minimized&nbsp;with&nbsp;respect&nbsp;to&nbsp;this<br>
selected&nbsp;functional)&nbsp;Notice&nbsp;that&nbsp;the&nbsp;electronic&nbsp;energy&nbsp;is&nbsp;also<br>
evaluated&nbsp;non-selfconsistently&nbsp;by&nbsp;DACAPO&nbsp;for&nbsp;other<br>
exchange-correlation&nbsp;functionals&nbsp;Recognized&nbsp;options&nbsp;:<br>
&nbsp;<br>
*&nbsp;"PZ"&nbsp;(Perdew&nbsp;Zunger&nbsp;LDA-parametrization)<br>
*&nbsp;"VWN"&nbsp;(Vosko&nbsp;Wilk&nbsp;Nusair&nbsp;LDA-parametrization)<br>
*&nbsp;"PW91"&nbsp;(Perdew&nbsp;Wang&nbsp;91&nbsp;GGA-parametrization)<br>
*&nbsp;"PBE"&nbsp;(Perdew&nbsp;Burke&nbsp;Ernzerhof&nbsp;GGA-parametrization)<br>
*&nbsp;"revPBE"&nbsp;(revised&nbsp;PBE/1&nbsp;GGA-parametrization)<br>
*&nbsp;"RPBE"&nbsp;(revised&nbsp;PBE/2&nbsp;GGA-parametrization)<br>
&nbsp;<br>
option&nbsp;"PZ"&nbsp;is&nbsp;not&nbsp;allowed&nbsp;for&nbsp;spin&nbsp;polarized<br>
calculation;&nbsp;use&nbsp;"VWN"&nbsp;instead.</tt></dd></dl>

<dl><dt><a name="Jacapo-strip"><strong>strip</strong></a>(self)</dt><dd><tt>remove&nbsp;all&nbsp;large&nbsp;memory&nbsp;nc&nbsp;variables&nbsp;not&nbsp;needed&nbsp;for<br>
anything&nbsp;I&nbsp;use&nbsp;very&nbsp;often.</tt></dd></dl>

<dl><dt><a name="Jacapo-update_input_parameters"><strong>update_input_parameters</strong></a>(self)</dt><dd><tt>read&nbsp;in&nbsp;all&nbsp;the&nbsp;input&nbsp;parameters&nbsp;from&nbsp;the&nbsp;netcdfile</tt></dd></dl>

<dl><dt><a name="Jacapo-write"><strong>write</strong></a>(self, new<font color="#909090">=False</font>)</dt><dd><tt>write&nbsp;out&nbsp;everything&nbsp;to&nbsp;the&nbsp;ncfile&nbsp;:&nbsp;<a href="#Jacapo-get_nc">get_nc</a>()<br>
&nbsp;<br>
new&nbsp;determines&nbsp;whether&nbsp;to&nbsp;delete&nbsp;any&nbsp;existing&nbsp;ncfile,&nbsp;and&nbsp;rewrite&nbsp;it.</tt></dd></dl>

<dl><dt><a name="Jacapo-write_input"><strong>write_input</strong></a>(self)</dt><dd><tt>write&nbsp;out&nbsp;input&nbsp;parameters&nbsp;as&nbsp;needed<br>
&nbsp;<br>
you&nbsp;must&nbsp;define&nbsp;a&nbsp;self.<strong>_set_keyword</strong>&nbsp;function&nbsp;that&nbsp;does&nbsp;all&nbsp;the<br>
actual&nbsp;writing.</tt></dd></dl>

<dl><dt><a name="Jacapo-write_nc"><strong>write_nc</strong></a>(self, nc<font color="#909090">=None</font>, atoms<font color="#909090">=None</font>)</dt><dd><tt>write&nbsp;out&nbsp;atoms&nbsp;to&nbsp;a&nbsp;netcdffile.<br>
&nbsp;<br>
This&nbsp;does&nbsp;not&nbsp;write&nbsp;out&nbsp;the&nbsp;calculation&nbsp;parameters!<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;nc&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;ncfilename&nbsp;to&nbsp;write&nbsp;to.&nbsp;this&nbsp;file&nbsp;will&nbsp;get&nbsp;clobbered<br>
&nbsp;&nbsp;&nbsp;&nbsp;if&nbsp;it&nbsp;already&nbsp;exists.<br>
&nbsp;<br>
&nbsp;&nbsp;atoms&nbsp;:&nbsp;ASE.Atoms<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms&nbsp;to&nbsp;write.&nbsp;if&nbsp;None&nbsp;use&nbsp;the&nbsp;attached&nbsp;atoms<br>
&nbsp;&nbsp;&nbsp;&nbsp;if&nbsp;no&nbsp;atoms&nbsp;are&nbsp;attached&nbsp;only&nbsp;the&nbsp;calculator&nbsp;is<br>
&nbsp;&nbsp;&nbsp;&nbsp;written&nbsp;out.<br>
&nbsp;<br>
the&nbsp;ncfile&nbsp;is&nbsp;always&nbsp;opened&nbsp;in&nbsp;'a'&nbsp;mode.<br>
&nbsp;<br>
note:&nbsp;it&nbsp;is&nbsp;good&nbsp;practice&nbsp;to&nbsp;use&nbsp;the&nbsp;atoms&nbsp;argument&nbsp;to&nbsp;make<br>
sure&nbsp;that&nbsp;the&nbsp;geometry&nbsp;you&nbsp;mean&nbsp;gets&nbsp;written!&nbsp;Otherwise,&nbsp;the<br>
atoms&nbsp;in&nbsp;the&nbsp;calculator&nbsp;is&nbsp;used,&nbsp;which&nbsp;may&nbsp;be&nbsp;different&nbsp;than<br>
the&nbsp;external&nbsp;copy&nbsp;of&nbsp;the&nbsp;atoms.</tt></dd></dl>

<hr>
Static methods defined here:<br>
<dl><dt><a name="Jacapo-read_atoms"><strong>read_atoms</strong></a>(filename)</dt><dd><tt>read&nbsp;atoms&nbsp;and&nbsp;calculator&nbsp;from&nbsp;an&nbsp;existing&nbsp;netcdf&nbsp;file.<br>
&nbsp;<br>
:Parameters:<br>
&nbsp;<br>
&nbsp;&nbsp;filename&nbsp;:&nbsp;string<br>
&nbsp;&nbsp;&nbsp;&nbsp;name&nbsp;of&nbsp;file&nbsp;to&nbsp;read&nbsp;from.<br>
&nbsp;<br>
static&nbsp;method<br>
&nbsp;<br>
example::<br>
&nbsp;<br>
&nbsp;&nbsp;&gt;&gt;&gt;&nbsp;atoms&nbsp;=&nbsp;<a href="#Jacapo">Jacapo</a>.<a href="#Jacapo-read_atoms">read_atoms</a>(ncfile)<br>
&nbsp;&nbsp;&gt;&gt;&gt;&nbsp;calc&nbsp;=&nbsp;atoms.get_calculator()<br>
&nbsp;<br>
this&nbsp;method&nbsp;is&nbsp;here&nbsp;for&nbsp;legacy&nbsp;purposes.&nbsp;I&nbsp;used&nbsp;to&nbsp;use&nbsp;it&nbsp;alot.</tt></dd></dl>

<hr>
Data and other attributes defined here:<br>
<dl><dt><strong>__version__</strong> = '0.4'</dt></dl>

<dl><dt><strong>default_input</strong> = {'ados': None, 'ascii_debug':
'Off', 'atoms': None, 'calculate_stress': False, 'charge_mixing':
{'method': 'Pulay', 'mixingcoeff': 0.1, 'mixinghistory': 10,
'precondition': 'No', 'updatecharge': 'Yes'}, 'convergence':
{'density': 0.0001, 'energy': 1e-05, 'maxsteps': None, 'maxtime': None,
'occupation': 0.001}, 'decoupling': None, 'dipole': {'adddipfield':
0.0, 'initval': 0.0, 'mixpar': 0.2, 'position': None, 'status': False},
'dw': 350, 'electronic_minimization': {'diagsperband': 2, 'method':
'eigsolve'}, ...}</dt></dl>

</td></tr></tbody></table></p></td></tr></tbody></table></p><p>
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<tbody>
    
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt><a name="-read"><strong>read</strong></a>(ncfile)</dt><dd><tt>return&nbsp;atoms&nbsp;and&nbsp;calculator&nbsp;from&nbsp;ncfile<br>
&nbsp;<br>
&gt;&gt;&gt;&nbsp;atoms,&nbsp;calc&nbsp;=&nbsp;<a href="#-read">read</a>('co.nc')</tt></dd></dl>
</td></tr></tbody></table></p><p><br>
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