<div dir="ltr">Dear Matthias, <div><br></div><div>I tried your suggestion, </div><div>the transformation still occurs in the first step of the optimization , I also try just keeping using the default of FORMAT, it doesnt work </div><div><br></div><div>best, </div><div><br></div><div>Andres </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El lun, 24 abr 2023 a la(s) 21:21, Krack Matthias (<a href="mailto:matthias.krack@psi.ch">matthias.krack@psi.ch</a>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg6210757178985604662">
<div lang="DE" style="overflow-wrap: break-word;">
<div class="m_6210757178985604662WordSection1">
<p class="MsoNormal"><span lang="EN-GB">You can try to drop the keyword
</span><span lang="EN-GB">FORMAT DCD_ALIGNED_CELL or use just FORMAT DCD instead.</span><span lang="EN-GB"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB"><u></u> <u></u></span></p>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(225,225,225);padding:3pt 0cm 0cm">
<p class="MsoNormal" style="margin-left:35.4pt"><b>Von:</b> <a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>>
<b>Im Auftrag von </b><a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a><br>
<b>Gesendet:</b> Montag, 24. April 2023 19:16<br>
<b>An:</b> cp2k <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>><br>
<b>Betreff:</b> Re: [CP2K:18701] modification of CELL_ parameters<u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:35.4pt"><u></u> <u></u></p>
<p class="MsoNormal" style="margin-left:35.4pt">Dear Matthias, <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:35.4pt">this could be an example <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:35.4pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:35.4pt"><br>
&FORCE_EVAL<br>
&DFT<br>
BASIS_SET_FILE_NAME BASIS_MOLOPT<br>
BASIS_SET_FILE_NAME BASIS_MOLOPT_UCL<br>
CHARGE 0<br>
&MGRID<br>
CUTOFF 700<br>
NGRIDS 5<br>
REL_CUTOFF 70<br>
&END MGRID<br>
MULTIPLICITY 0<br>
&POISSON<br>
PERIODIC XYZ<br>
&END POISSON<br>
POTENTIAL_FILE_NAME GTH_POTENTIALS<br>
&PRINT<br>
&MO_CUBES<br>
ADD_LAST SYMBOLIC<br>
&EACH<br>
CELL_OPT 0<br>
GEO_OPT 0<br>
&END EACH<br>
NHOMO 1<br>
NLUMO 1<br>
WRITE_CUBE .FALSE.<br>
&END MO_CUBES<br>
&MULLIKEN ON<br>
ADD_LAST SYMBOLIC<br>
&EACH<br>
CELL_OPT 0<br>
GEO_OPT 0<br>
&END EACH<br>
&END MULLIKEN<br>
&END PRINT<br>
&QS<br>
EPS_DEFAULT 1e-12<br>
METHOD GPW<br>
&END QS<br>
&SCF<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:35.4pt">EPS_SCF 5e-08<br>
MAX_ITER_LUMO 5000<br>
MAX_SCF 80<br>
&MIXING<br>
ALPHA 0.4<br>
BETA 0.5<br>
METHOD DIRECT_P_MIXING<br>
&END MIXING<br>
&OT<br>
MINIMIZER CG<br>
PRECONDITIONER FULL_ALL<br>
&END OT<br>
&OUTER_SCF<br>
EPS_SCF 5e-08<br>
MAX_SCF 60<br>
&END OUTER_SCF<br>
&PRINT<br>
&RESTART<br>
BACKUP_COPIES 0<br>
&END RESTART<br>
&END PRINT<br>
&END SCF<br>
UKS .FALSE.<br>
&XC<br>
DENSITY_CUTOFF 1e-10<br>
GRADIENT_CUTOFF 1e-10<br>
TAU_CUTOFF 1e-10<br>
&VDW_POTENTIAL<br>
&PAIR_POTENTIAL<br>
PARAMETER_FILE_NAME dftd3.dat<br>
REFERENCE_FUNCTIONAL PBE<br>
R_CUTOFF 10.0<br>
TYPE DFTD3(BJ)<br>
&END PAIR_POTENTIAL<br>
POTENTIAL_TYPE PAIR_POTENTIAL<br>
&END VDW_POTENTIAL<br>
&XC_FUNCTIONAL<br>
&PBE<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:35.4pt"> PARAMETRIZATION ORIG<br>
&END PBE<br>
&END XC_FUNCTIONAL<br>
&END XC<br>
&END DFT<br>
METHOD QUICKSTEP<br>
STRESS_TENSOR ANALYTICAL<br>
&SUBSYS<br>
&CELL<br>
A -1.59515785 -2.7628944422923 -3.9070099102745e-16<br>
B -1.59515785 2.7628944422923 1.9535049551373e-16<br>
C 0.0 0.0 -14.879004<br>
MULTIPLE_UNIT_CELL 4 4 1<br>
&END CELL<br>
&KIND Mo<br>
BASIS_SET TZVP-MOLOPT-SR-GTH-q14<br>
POTENTIAL GTH-PBE-q14<br>
&END KIND<br>
&KIND S<br>
BASIS_SET DZVP-MOLOPT-SR-GTH-q6<br>
POTENTIAL GTH-PBE-q6<br>
&END KIND<br>
&TOPOLOGY<br>
COORD_FILE_FORMAT XYZ<br>
COORD_FILE_NAME <a href="http://aiida.coords.xyz" target="_blank">aiida.coords.xyz</a><br>
MULTIPLE_UNIT_CELL 4 4 1<br>
&END TOPOLOGY<br>
&END SUBSYS<br>
&END FORCE_EVAL<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:35.4pt">&GLOBAL<br>
ELPA_KERNEL GENERIC<br>
PRINT_LEVEL MEDIUM<br>
PROJECT aiida<br>
RUN_TYPE CELL_OPT<br>
&END GLOBAL<br>
&MOTION<br>
&CELL_OPT<br>
&BFGS<br>
TRUST_RADIUS [angstrom] 0.2<br>
&END BFGS<br>
EXTERNAL_PRESSURE [bar] 0.0<br>
KEEP_ANGLES .TRUE.<br>
KEEP_SYMMETRY .FALSE.<br>
MAX_DR [bohr] 0.0005<br>
MAX_FORCE [bohr^-1*hartree] 0.00010<br>
MAX_ITER 1000<br>
OPTIMIZER BFGS<br>
PRESSURE_TOLERANCE [bar] 100<br>
RMS_DR [bohr] 0.0005<br>
RMS_FORCE [bohr^-1*hartree] 0.00010<br>
TYPE DIRECT_CELL_OPT<br>
&END CELL_OPT<br>
&GEO_OPT<br>
&BFGS<br>
TRUST_RADIUS [angstrom] 0.20<br>
&END BFGS<br>
MAX_DR [bohr] 0.0005<br>
MAX_FORCE [bohr^-1*hartree] 0.00010<br>
MAX_ITER 1000<br>
OPTIMIZER BFGS<br>
RMS_DR [bohr] 0.0005<br>
RMS_FORCE [bohr^-1*hartree] 0.00010<br>
TYPE MINIMIZATION<br>
&END GEO_OPT<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-right:0cm;margin-bottom:12pt;margin-left:35.4pt">
&PRINT<br>
&RESTART<br>
BACKUP_COPIES 0<br>
&EACH<br>
CELL_OPT 1<br>
GEO_OPT 1<br>
MD 1<br>
&END EACH<br>
&END RESTART<br>
&TRAJECTORY<br>
&EACH<br>
CELL_OPT 1<br>
GEO_OPT 1<br>
MD 1<br>
&END EACH<br>
FORMAT DCD_ALIGNED_CELL<br>
&END TRAJECTORY<br>
&END PRINT<br>
&END MOTION<br>
161,1 Bot<u></u><u></u></p>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:35.4pt">El lunes, 24 de abril de 2023 a la(s) 18:08:49 UTC+2, Krack Matthias escribió:<u></u><u></u></p>
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<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin-left:4.8pt;margin-right:0cm">
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<div>
<p class="MsoNormal" style="margin-left:35.4pt">
<span lang="EN-GB">Without the full input, it is difficult to give further hints.</span><u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:35.4pt">
<span lang="EN-GB"> </span><u></u><u></u></p>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(225,225,225);padding:3pt 0cm 0cm">
<p class="MsoNormal" style="margin-left:70.8pt">
<b>Von:</b> <span class="m_6210757178985604662MsoHyperlink"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a></span> <<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a></span>>
<b>Im Auftrag von </b><span class="m_6210757178985604662MsoHyperlink"><a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a></span><br>
<b>Gesendet:</b> Montag, 24. April 2023 17:30<br>
<b>An:</b> cp2k <<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a></span>><br>
<b>Betreff:</b> Re: [CP2K:18699] modification of CELL_ parameters<u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:70.8pt">
<u></u><u></u></p>
<p class="MsoNormal" style="margin-left:70.8pt">
Dear Mathias, <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:70.8pt">
<u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:70.8pt">
I tried the KEEP_ANGLES, and indeed it keeps the cell vectors, but only the first step, after that it applies the same transformation . <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:70.8pt">
<u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:70.8pt">
CELL_REF| Volume [angstrom^3]: 2098.417005<br>
CELL_REF| Vector a [angstrom -6.381 -11.052 -0.000 |a| = 12.761263<br>
CELL_REF| Vector b [angstrom -6.381 11.052 0.000 |b| = 12.761263<br>
CELL_REF| Vector c [angstrom 0.000 0.000 -14.879 |c| = 14.879004<br>
CELL_REF| Angle (b,c), alpha [degree]: 90.000000<br>
CELL_REF| Angle (a,c), beta [degree]: 90.000000<br>
CELL_REF| Angle (a,b), gamma [degree]: 120.000000<br>
CELL_REF| Numerically orthorhombic: NO<br>
CELL_OPT| Pressure tolerance [bar]: 100.0<br>
CELL_OPT| Keep angles between the cell vectors: YES<br>
CELL_OPT| Keep cell symmetry: NO<br>
CELL_OPT| Constraint: NONE<br>
*** STARTING CELL OPTIMIZATION ***<br>
CELL| Volume [angstrom^3]: 2098.417005<br>
CELL| Vector a [angstrom]: 12.761 0.000 0.000 |a| = 12.761263<br>
CELL| Vector b [angstrom]: -6.381 11.052 0.000 |b| = 12.761263<br>
CELL| Vector c [angstrom]: 0.000 0.000 14.879 |c| = 14.879004<br>
CELL| Angle (b,c), alpha [degree]: 90.000000<br>
CELL| Angle (a,c), beta [degree]: 90.000000<br>
CELL| Angle (a,b), gamma [degree]: 120.000000<br>
CELL| Numerically orthorhombic: NO<br>
CELL| Volume [angstrom^3]: 2083.849671<br>
CELL| Vector a [angstrom]: 12.727 0.000 0.000 |a| = 12.726904<br>
CELL| Vector b [angstrom]: -6.363 11.022 0.000 |b| = 12.726904<br>
CELL| Vector c [angstrom]: 0.000 0.000 14.856 |c| = 14.855602<br>
CELL| Angle (b,c), alpha [degree]: 90.000000<br>
CELL| Angle (a,c), beta [degree]: 90.000000<br>
CELL| Angle (a,b), gamma [degree]: 120.000000<br>
CELL| Numerically orthorhombic: NO<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:70.8pt">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:70.8pt">
I wonder if is possible to stop this behaviour , <u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:70.8pt">
<u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:70.8pt">
best, <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:70.8pt">
<u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:70.8pt">
Andres Ortega<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:70.8pt">
<u></u><u></u></p>
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<div>
<div>
<p class="MsoNormal" style="margin-left:70.8pt">
El lunes, 24 de abril de 2023 a la(s) 17:09:45 UTC+2, Krack Matthias escribió:<u></u><u></u></p>
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<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin:5pt 0cm 5pt 4.8pt">
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<div>
<p class="MsoNormal" style="margin-left:70.8pt">
<span lang="EN-US">Yes, you can try KEEP_ANGLES, but this is not exactly the same constraint, because a and b are allowed to differ in length.</span><u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:70.8pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:70.8pt">
<span lang="EN-US">Matthias</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:70.8pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm">
<p class="MsoNormal" style="margin-bottom:12pt;margin-left:106.8pt">
<b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black"><span class="m_6210757178985604662MsoHyperlink"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a></span> <<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a></span>> on behalf of
<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a></span> <<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a></span>><br>
<b>Date: </b>Monday, 24 April 2023 at 16:56<br>
<b>To: </b>cp2k <<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a></span>><br>
<b>Subject: </b>Re: [CP2K:18697] modification of CELL_ parameters</span><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:106.8pt">
Dear Mathias , <u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:106.8pt">
thank you for your email <u></u><u></u></p>
</div>
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<p class="MsoNormal" style="margin-left:106.8pt">
<u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:106.8pt">
However how can I make a cell opt, where I keep the symmetry, <u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:106.8pt">
then I should just use KEEP_ANGLES , will it be enough?<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:106.8pt">
<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:106.8pt">
best <u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:106.8pt">
<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:106.8pt">
Andres <u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:106.8pt">
<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:106.8pt">
El lunes, 24 de abril de 2023 a la(s) 16:40:52 UTC+2, Krack Matthias escribió:<u></u><u></u></p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin:5pt 0cm 5pt 4.8pt">
<div>
<div>
<p class="MsoNormal" style="margin-left:106.8pt">
<span lang="DE-CH">Hi Andres</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:106.8pt">
<span lang="DE-CH"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:106.8pt">
<span lang="EN-US">The keyword </span>SYMMETRY MONOCLINIC_GAMMA_AB<span lang="EN-US"> changes the cell as requested. Drop that keyword, if you want to keep the cell vectors from your input.</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:106.8pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:106.8pt">
<span lang="EN-US">HTH</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:106.8pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:106.8pt">
<span lang="EN-US">Matthias</span><u></u><u></u></p>
</div>
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<div>
<div>
<p class="MsoNormal" style="margin-left:106.8pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm">
<p class="MsoNormal" style="margin-bottom:12pt;margin-left:142.8pt">
<b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black"><span class="m_6210757178985604662MsoHyperlink"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a></span> <<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a></span>> on behalf of
<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a></span> <<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a></span>><br>
<b>Date: </b>Monday, 24 April 2023 at 16:33<br>
<b>To: </b>cp2k <<span class="m_6210757178985604662MsoHyperlink"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a></span>><br>
<b>Subject: </b>[CP2K:18695] modification of CELL_ parameters</span><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:142.8pt">
Dear Cp2k users and developers, <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:142.8pt">
<u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:142.8pt">
I was wondering if you could help me with a doubt i have , <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:142.8pt">
does cp2k modifies the cell vectors (applies an operation to them) once you set up a cell opt calculations <u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:142.8pt">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:142.8pt">
for example <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:142.8pt">
say you have a systems with these cell parameters in the input file <u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:142.8pt">
&CELL<br>
A -1.59515785 -2.7628944422923 -3.9070099102745e-16<br>
B -1.59515785 2.7628944422923 1.9535049551373e-16<br>
C 0.0 0.0 -14.879004<br>
MULTIPLE_UNIT_CELL 4 4 1<br>
SYMMETRY MONOCLINIC_GAMMA_AB<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:142.8pt">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:142.8pt">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:142.8pt">
but once the simulations starts it becomes <u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:142.8pt">
<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:142.8pt">
CELL_TOP| Volume [angstrom^3]: 2098.417005<br>
CELL_TOP| Vector a [angstrom 12.761 0.000 0.000 |a| = 12.761263<br>
CELL_TOP| Vector b [angstrom -6.381 11.052 0.000 |b| = 12.761263<br>
CELL_TOP| Vector c [angstrom 0.000 0.000 14.879 |c| = 14.879004<br>
CELL_TOP| Angle (b,c), alpha [degree]: 90.000000<br>
CELL_TOP| Angle (a,c), beta [degree]: 90.000000<br>
CELL_TOP| Angle (a,b), gamma [degree]: 120.000000<br>
CELL_TOP| Requested initial symmetry: MONOCLINIC_GAMMA_AB<br>
CELL_TOP| Numerically orthorhombic: NO<u></u><u></u></p>
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<u></u><u></u></p>
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So if you notices the magnitudes are the same but vector a, and b are in a different basis. <u></u><u></u></p>
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Is there a way to avoid this ? <u></u><u></u></p>
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<u></u><u></u></p>
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best<u></u><u></u></p>
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<u></u><u></u></p>
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Andres Ortega<u></u><u></u></p>
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<u></u><u></u></p>
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