[CPMD-list] cell parameter
Axel Kohlmeyer
axel.kohlmeyer at theochem.ruhr-uni-bochum.de
Sun Oct 10 14:49:32 CEST 2004
On 10 Oct 2004, sanjeev narooka wrote:
SN> hi all user,
sanjeev,
first one remark. please don't send html or otherwise encoded
text to mailing lists. many people, that use simple (and fast)
mail readers will see something like the few lines quoted below.
it will take extra work to decode and read it, so chances are
higher, that your mail will be ignored.
==quote==
<P>=0Ahi all user,<BR>=0A <BR>=0Ai would like to ask some question about ce=
ll parameter.a sample input file of cpmd-test is attached.<BR>=0A<BR>=0A1-i=
f i would have to simulate 64 molecules of water then should i =
increase the cell length and keep the all atom in one unit cell or =
i must repeat this unit cell in x,y,z direction.<BR>=0A<BR>=0A2-atomic coor=
dinates in cpmd run is arbitrary or it must be the same as in real material=
and should we take the bond length into account also while writing atomic =
coordinates.<BR>=0A<BR>=0A3- should we change the parameter in Goedecker ps=
eudopotential file accordingly our system or it must be used as it is while=
runnig cpmd.x<BR>=0A<BR>=0A4-in Axel kohlmeyer web page of water simulatio=
==end quote==
SN> i would like to ask some question about cell parameter.a sample input
SN> file of cpmd-test is attached.
SN> 1-if i would have to simulate 64 molecules of water then should i
SN> increase the cell length and keep the all atom in one unit cell or i
SN> must repeat this unit cell in x,y,z direction.
ok, there is some vital information missing here: what _density_
of water do you want to simulate? assuming you want to have the
same density as in the given example, then you have to decide, whether
you want to keep your supercell cubic or not (most likely yes).
depending on that coice, you will have to add coordinates for the
newly added water molecules. if you just increase the lattice constant
for the example given, which has fractional coordinates, all atom
coordinates with be stretched accordingly. now if you add new atoms,
you will have to increase the number of atoms per species properly,
but of course you will also have to equilibrate your system.
before asking any further questions, i'd recommend you read about
the CELL, SCALE, ANSTROM, SYMMETRY keywords, as well as the
'Further details of the input' section in the manual.
SN> 2-atomic coordinates in cpmd run is arbitrary or it must be the same
SN> as in real material and should we take the bond length into account
SN> also while writing atomic coordinates.
i don't know what bond length you are referring to, but coordinates
are quite arbitrary. only, if your coordinates are outside of the
supercell, cpmd will translated them back into the supercell according
to the periodic boundary conditions.
SN> 3- should we change the parameter in Goedecker pseudopotential file
SN> accordingly our system or it must be used as it is while runnig cpmd.x
you should _never_ change a parameter in a pseudopotential file
unless you really know what you are doing. what parameter are you
referring to, anyway?
SN> 4-in Axel kohlmeyer web page of water simulation which is as follows
TEMPCONTROL IONS
400.0 50.0
NOSE IONS MASSIVE
400.0 2500.0
NOSE ELECTRONS
0.02 10000.0
SN> the value after 400.0 (eg 0 50.0 and again in fourth line 2500.0,0.02
SN> 10000.0 )stands for what.
these parameters are covered in detail in the manual.
the second parameter in TEMPCONTROL is the maximum value
which the instantaneous temperature may deviate from the
desired temperature before the kinetic energy is scaled.
(so in case your temperature is above 450K velocities
will be scaled back to have a temperture of 400K. similarly
it will be scaled up for 350K and below).
for the nose hoover chains the second parameter is the
frequency of a mode (in cm^-1) to which the thermostat
couples (it should be close enough to a real existing
mode, so that the thermostat can actually exchange energy
with the system).
best regards,
axel kohlmeyer.
SN> the input file is as
thanking in advance
&CPMD
LINEAR RESPONSE
&END
&RESP
NMR FULL
&END
&DFT
NEWCODE
FUNCTIONAL BLYP
&END
&SYSTEM
SCALE
SYMMETRY
1
CELL
18.64215 1. 1. 0.0 0.0 0.0
CUTOFF
70.0
&END
&ATOMS
*O_SG_BLYP
LMAX=P
32
-0.36687 0.51547 0.03858
0.04654 0.42373 -0.04132
-0.13264 0.09788 -0.49158
-0.25283 -0.25274 0.45476
0.43036 0.11249 -0.04015
0.23774 -0.24561 0.02796
-0.28373 -0.34919 -0.26897
-0.15847 0.32543 -0.31740
0.50630 0.41162 0.27446
0.41580 -0.04854 0.19495
0.08208 -0.04073 -0.26788
-0.08967 0.16763 0.10464
0.36541 0.04422 -0.37853
-0.24265 0.30156 -0.06024
0.00047 -0.24284 0.35250
0.09506 -0.55455 -0.36671
0.39353 -0.24187 -0.21652
-0.42713 -0.05290 0.43525
-0.38096 0.41897 0.54761
0.37563 0.34558 -0.33718
0.11451 -0.45557 0.22547
0.17722 0.02419 0.34017
0.37501 -0.36704 0.39345
-0.35986 0.04083 -0.16910
-0.39713 -0.26661 0.19022
0.19576 -0.28820 -0.40144
0.28723 0.26210 0.22348
-0.11113 0.30823 0.31810
-0.05683 -0.20771 -0.10124
0.11165 0.12286 -0.05824
-0.24203 -0.06256 0.05471
0.37397 0.38911 -0.07478
*H_SG_BLYP KLEINMAN-BYLANDER
LMAX=S
64
-0.33036 0.42744 0.01260
-0.43687 0.52649 -0.02956
0.04821 0.32692 -0.06064
0.07111 0.45994 -0.13416
-0.19998 0.02540 -0.49628
-0.16229 0.16696 -0.42452
-0.15541 -0.24373 0.44032
-0.27038 -0.31065 0.53274
0.42345 0.21566 -0.04571
0.50315 0.08669 -0.10635
0.24104 -0.16838 0.09154
0.27734 -0.21270 -0.05481
-0.29597 -0.44288 -0.30877
-0.22246 -0.35342 -0.19231
-0.07141 0.38057 -0.33217
-0.17185 0.30439 -0.21669
0.43361 0.34407 0.25517
0.54796 0.43641 0.18698
0.42338 0.02443 0.12512
0.45449 -0.13345 0.16167
0.00557 -0.09032 -0.22263
0.03667 -0.00765 -0.35092
0.00120 0.14802 0.06645
-0.08946 0.19313 0.20159
0.44473 0.01796 -0.44288
0.38415 -0.01964 -0.30771
-0.17018 0.25293 0.00264
-0.30909 0.22815 -0.07579
0.01831 -0.31367 0.28970
0.04909 -0.15944 0.33024
0.08338 -0.45561 -0.38034
0.18663 -0.58347 -0.36502
0.48793 -0.26627 -0.23565
0.32799 -0.26728 -0.29317
-0.35933 -0.11956 0.42477
-0.45229 -0.01660 0.33842
-0.39877 0.41868 0.45006
-0.29225 0.37468 0.56028
0.36945 0.24330 -0.33394
0.46084 0.37476 -0.39002
0.11297 -0.49470 0.13648
0.19937 -0.40306 0.22579
0.25604 -0.01084 0.28759
0.20941 0.03418 0.43970
0.41735 -0.45369 0.37468
0.44813 -0.30628 0.36818
-0.34398 0.01399 -0.26427
-0.29967 -0.00926 -0.10610
-0.33742 -0.29725 0.25792
-0.39618 -0.33553 0.11503
0.24877 -0.29745 -0.48400
0.16575 -0.19530 -0.38117
0.23171 0.19934 0.28238
0.23863 0.35401 0.24424
-0.08092 0.25840 0.40210
-0.08356 0.40365 0.31610
-0.11742 -0.17357 -0.03339
0.02448 -0.23447 -0.05246
0.20746 0.11886 -0.04180
0.09779 0.07429 -0.14676
-0.29713 -0.10067 0.12577
-0.17966 0.00788 0.09390
0.28490 0.40502 -0.03547
0.36553 0.38939 -0.17630
&END
--
=======================================================================
Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de
Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
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