Guidance on Repeated Element Symbols in POSCAR File and POTCAR Generation.

[hszhao.cn@gmail.com]

Hello VASP Community,

I have encountered a VASP POSCAR file that lists element symbols in a manner I'm unfamiliar with, where some element symbols are repeated rather than being grouped with each type of element appearing only once. See below for more information:

Code: Select all

$ cat Au31MoS2Mo26S52
Au Mo S  Mo S 
 1.0000000000000000
    10.3283760837150886   12.7662618209248180    0.0000000000000000
   -16.2200945810751165    2.5615055783906477    0.0000000000000000
     0.0000000000000000    0.0000000000000000   22.1610999999999976
 Au  Mo  S   Mo  S  
  31   1   2  26  52
Cartesian
 -0.0000000065855675  0.0000000010400043  0.0000000000000000
 -13.2707768783351749  2.5601744158490893  0.0000000000000000
 -11.7949652034572612  5.1136930127503666  0.0000000000000000
 -10.3191535285793492  7.6672116096516421  0.0000000000000000
 -8.8433418537014266 10.2207302065529202  0.0000000000000000
 -7.3675301788235155 12.7742488034541939  0.0000000000000000
 -10.3214591690096746  2.5588432522675286  0.0000000000000000
 -8.8456474941317556  5.1123618491688054  0.0000000000000000
 -7.3698358192538409  7.6658804460700791  0.0000000000000000
 -5.8940241443759236 10.2193990429713573  0.0000000000000000
 -4.4182124694980054 12.7729176398726310  0.0000000000000000
 -7.3721414596841672  2.5575120886859661  0.0000000000000000
 -5.8963297848062508  5.1110306855872416  0.0000000000000000
 -4.4205181099283379  7.6645492824885171  0.0000000000000000
 -2.9447064350504171 10.2180678793897961  0.0000000000000000
 -1.4688947601724982 12.7715864762910716  0.0000000000000000
 -4.4228237503586616  2.5561809251044050  0.0000000000000000
 -2.9470120754807456  5.1096995220056804  0.0000000000000000
 -1.4712004006028285  7.6632181189069559  0.0000000000000000
  0.0046112742750913 10.2167367158082367  0.0000000000000000
  1.4804229491530048 12.7702553127095122  0.0000000000000000
 -1.4735060410331566  2.5548497615228425  0.0000000000000000
  0.0023056338447619  5.1083683584241202  0.0000000000000000
  1.4781173087226764  7.6618869553253939  0.0000000000000000
  2.9539289836005942 10.2154055522266702  0.0000000000000000
  4.4297406584785124 12.7689241491279457  0.0000000000000000
  1.4758116682923490  2.5535185979412809  0.0000000000000000
  2.9516233431702652  5.1070371948425572  0.0000000000000000
  4.4274350180481816  7.6605557917438318  0.0000000000000000
  5.9032466929260980 10.2140743886451109  0.0000000000000000
  7.3790583678040171 12.7675929855463846  0.0000000000000000
  1.1475973384415563  1.4184735304750473  5.5805500000000032
 -0.0000000065855675  0.0000000010400043  7.1610999999999985
 -0.0000000065855675  0.0000000010400043  4.0000000000000000
 -9.6657990489418566  3.1261439160688131  5.5805500000000032
 -12.1226671687679826  5.1138409135917131  5.5805500000000032
 -4.2591008552501499  2.2723087232719301  5.5805500000000032
 -6.7159689750762794  4.2600057207948323  5.5805500000000032
 -9.1728370949024036  6.2477027183177309  5.5805500000000032
 -1.3092707813845714  3.4061705279979488  5.5805500000000032
 -3.7661389012106996  5.3938675255208501  5.5805500000000032
 -6.2230070210368256  7.3815645230437514  5.5805500000000032
 -8.6798751408629542  9.3692615205666527  5.5805500000000032
  1.6405592924810080  4.5400323327239676  5.5805500000000032
 -0.8163088273451201  6.5277293302468689  5.5805500000000032
 -3.2731769471712493  8.5154263277697702  5.5805500000000032
 -5.7300450669973699 10.5031233252926732  5.5805500000000032
  4.5903893663465869  5.6738941374499863  5.5805500000000032
  2.1335212465204600  7.6615911349728885  5.5805500000000032
 -0.3233468733056687  9.6492881324957889  5.5805500000000032
 -2.7802149931317950 11.6369851300186937  5.5805500000000032
 -5.2370831129579223 13.6246821275415932  5.5805500000000032
  5.0833513203860399  8.7954529396989081  5.5805500000000032
  2.6264832005599090 10.7831499372218076  5.5805500000000032
  0.1696150807337818 12.7708469347447089  5.5805500000000032
 -2.2872530390923491 14.7585439322676102  5.5805500000000032
  8.0331813942516170  9.9293147444249286  5.5805500000000032
  5.5763132744254866 11.9170117419478228  5.5805500000000032
  3.1194451545993624 13.9047087394707276  5.5805500000000032
  8.5261433482910736 13.0508735466738504  5.5805500000000032
 -10.8133963939689774  1.7076703866337695  7.1610999999999985
 -13.2702645137951105  3.6953673841566719  7.1610999999999985
 -5.4066982002772725  0.8538351938368869  7.1610999999999985
 -7.8635663201033994  2.8415321913597893  7.1610999999999985
 -10.3204344399295262  4.8292291888826897  7.1610999999999985
 -2.4568681264116945  1.9876969985629060  7.1610999999999985
 -4.9137362462378213  3.9753939960858080  7.1610999999999985
 -7.3706043660639473  5.9630909936087093  7.1610999999999985
 -9.8274724858900768  7.9507879911316115  7.1610999999999985
  0.4929619474538839  3.1215588032889245  7.1610999999999985
 -1.9639061723722426  5.1092558008118267  7.1610999999999985
 -4.4207742921983710  7.0969527983347280  7.1610999999999985
 -6.8776424120244943  9.0846497958576311  7.1610999999999985
  3.4427920213194634  4.2554206080149442  7.1610999999999985
  0.9859239014933353  6.2431176055378454  7.1610999999999985
 -1.4709442183327903  8.2308146030607485  7.1610999999999985
 -3.9278123381589176 10.2185116005836480  7.1610999999999985
 -6.3846804579850449 12.2062085981065511  7.1610999999999985
  3.9357539753589155  7.3769794102638633  7.1610999999999985
  1.4788858555327895  9.3646764077867655  7.1610999999999985
 -0.9779822642933425 11.3523734053096650  7.1610999999999985
 -3.4348503841194682 13.3400704028325681  7.1610999999999985
  6.8855840492244944  8.5108412149898829  7.1610999999999985
  4.4287159293983640 10.4985382125127806  7.1610999999999985
  1.9718478095722380 12.4862352100356855  7.1610999999999985
  7.3785460032639465 11.6324000172388047  7.1610999999999985
 -10.8133963939689774  1.7076703866337695  4.0000000000000000
 -13.2702645137951105  3.6953673841566719  4.0000000000000000
 -5.4066982002772725  0.8538351938368869  4.0000000000000000
 -7.8635663201033994  2.8415321913597893  4.0000000000000000
 -10.3204344399295262  4.8292291888826897  4.0000000000000000
 -2.4568681264116945  1.9876969985629060  4.0000000000000000
 -4.9137362462378213  3.9753939960858080  4.0000000000000000
 -7.3706043660639473  5.9630909936087093  4.0000000000000000
 -9.8274724858900768  7.9507879911316115  4.0000000000000000
  0.4929619474538839  3.1215588032889245  4.0000000000000000
 -1.9639061723722426  5.1092558008118267  4.0000000000000000
 -4.4207742921983710  7.0969527983347280  4.0000000000000000
 -6.8776424120244943  9.0846497958576311  4.0000000000000000
  3.4427920213194634  4.2554206080149442  4.0000000000000000
  0.9859239014933353  6.2431176055378454  4.0000000000000000
 -1.4709442183327903  8.2308146030607485  4.0000000000000000
 -3.9278123381589176 10.2185116005836480  4.0000000000000000
 -6.3846804579850449 12.2062085981065511  4.0000000000000000
  3.9357539753589155  7.3769794102638633  4.0000000000000000
  1.4788858555327895  9.3646764077867655  4.0000000000000000
 -0.9779822642933425 11.3523734053096650  4.0000000000000000
 -3.4348503841194682 13.3400704028325681  4.0000000000000000
  6.8855840492244944  8.5108412149898829  4.0000000000000000
  4.4287159293983640 10.4985382125127806  4.0000000000000000
  1.9718478095722380 12.4862352100356855  4.0000000000000000
  7.3785460032639465 11.6324000172388047  4.0000000000000000
 

My questions are twofold:

1. Is this method of listing the same elements repeatedly valid in VASP input files?
2. Assuming the format is acceptable, what would be the recommended approach for generating the corresponding POTCAR file? Specifically, how should one handle repeating elements in the sequence when concatenating the individual POTCAR files for each element?

I appreciate the insights and any guidance you can provide on handling such file configurations for VASP calculation.

Best regards,
Zhao

[merzuk.kaltak]

Dear Zhao,

the POSCAR you posted is valid.
To create a compatible POTCAR file you need to concatenate the individual POTCAR files in same order as they appear in the POSCAR.
In your case this means:

Code: Select all

cat POTCAR.Au POTCAR.Mo POTCAR.S POTCAR.Mo POTCAR.S > POTCAR

There can be various reasons why you want a species repeatedly defined in the POSCAR.
For instance, if you are interested in setting LDAUU to a value of 3 on the first Mo in your POSCAR only,
you could do that with following setting in the INCAR

Code: Select all

LDAUU = 0 3 0 0 0 

[hszhao.cn@gmail.com]

Dear merzuk.kaltak,

So, if I write this POSCASR in normal form, aka, all kinds of atoms of the same type in consecutive lines then how do I set LDAUU here?

[hszhao.cn@gmail.com]

Dear merzuk.kaltak,

More specifically, if I write my original POSCAR in the following format:

Code: Select all

$ cat Au31MoS2Mo26S52 
POSCAR file written by OVITO Basic 3.10.2
1
10.3283760837 12.7662618209 0.0
-16.2200945811 2.5615055784 0.0
0.0 0.0 22.1611
Au Mo S 
31 27 54 
Cartesian
-6.5855675e-09 1.0400043e-09 0.0
-13.2707768781 2.5601744156 0.0
-11.7949652029 5.1136930125 0.0
-10.3191535294 7.6672116096 0.0
-8.8433418542 10.2207302065 0.0
-7.3675301791 12.7742488034 0.0
-10.3214591686 2.5588432517 0.0
-8.8456474951 5.1123618489 0.0
-7.3698358199 7.6658804458 0.0
-5.8940241447 10.2193990427 0.0
-4.4182124696 12.7729176396 0.0
-7.3721414608 2.5575120882 0.0
-5.8963297856 5.1110306851 0.0
-4.4205181104 7.664549282 0.0
-2.9447064353 10.2180678789 0.0
-1.4688947601 12.7715864757 0.0
-4.4228237503 2.5561809256 0.0
-2.9470120751 5.1096995225 0.0
-1.4712003999 7.6632181194 0.0
0.0046112752 10.2167367163 0.0
1.4804229504 12.7702553132 0.0
-1.4735060408 2.5548497618 0.0
0.0023056344 5.1083683587 0.0
1.4781173095 7.6618869556 0.0
2.9539289831 10.2154055527 0.0
4.4297406583 12.7689241496 0.0
1.4758116687 2.5535185979 0.0
2.9516233439 5.1070371948 0.0
4.4274350174 7.660555792 0.0
5.9032466926 10.2140743889 0.0
7.3790583677 12.7675929858 0.0
1.1475973384 1.4184735304 5.5805500003
-9.6657990496 3.1261439161 5.5805500003
-12.1226671691 5.1138409134 5.5805500003
-4.2591008548 2.2723087231 5.5805500003
-6.715968976 4.2600057207 5.5805500003
-9.1728370956 6.247702718 5.5805500003
-1.3092707812 3.4061705277 5.5805500003
-3.7661389008 5.3938675251 5.5805500003
-6.223007022 7.3815645226 5.5805500003
-8.6798751416 9.36926152 5.5805500003
1.6405592924 4.5400323323 5.5805500003
-0.8163088272 6.5277293297 5.5805500003
-3.2731769484 8.5154263272 5.5805500003
-5.730045067 10.5031233258 5.5805500003
4.5903893659 5.6738941369 5.5805500003
2.1335212464 7.6615911343 5.5805500003
-0.3233468722 9.6492881329 5.5805500003
-2.7802149934 11.6369851305 5.5805500003
-5.237083113 13.6246821278 5.5805500003
5.083351321 8.7954529402 5.5805500003
2.6264832014 10.7831499375 5.5805500003
0.1696150802 12.7708469351 5.5805500003
-2.2872530394 14.7585439324 5.5805500003
8.0331813945 9.9293147448 5.5805500003
5.5763132749 11.9170117421 5.5805500003
3.1194451554 13.9047087394 5.5805500003
8.5261433485 13.0508735467 5.5805500003
-6.5855675e-09 1.0400043e-09 7.1611000006
-6.5855675e-09 1.0400043e-09 4.0
-10.8133963944 1.7076703867 7.1611000006
-13.270264514 3.695367384 7.1611000006
-5.4066981996 0.8538351937 7.1611000006
-7.8635663209 2.8415321913 7.1611000006
-10.3204344404 4.8292291886 7.1611000006
-2.4568681261 1.9876969983 7.1611000006
-4.9137362473 3.9753939959 7.1611000006
-7.3706043669 5.9630909933 7.1611000006
-9.8274724865 7.9507879906 7.1611000006
0.4929619475 3.121558803 7.1611000006
-1.9639061721 5.1092558003 7.1611000006
-4.4207742933 7.0969527979 7.1611000006
-6.8776424119 9.0846497965 7.1611000006
3.442792021 4.2554206076 7.1611000006
0.9859239015 6.2431176049 7.1611000006
-1.4709442187 8.2308146037 7.1611000006
-3.9278123383 10.2185116011 7.1611000006
-6.3846804579 12.2062085984 7.1611000006
3.9357539761 7.3769794108 7.1611000006
1.4788858565 9.3646764081 7.1611000006
-0.9779822647 11.3523734057 7.1611000006
-3.4348503843 13.340070403 7.1611000006
6.8855840496 8.5108412154 7.1611000006
4.4287159301 10.4985382127 7.1611000006
1.9718478089 12.4862352103 7.1611000006
7.3785460036 11.6324000173 7.1611000006
-10.8133963944 1.7076703867 4.0
-13.270264514 3.695367384 4.0
-5.4066981996 0.8538351937 4.0
-7.8635663209 2.8415321913 4.0
-10.3204344404 4.8292291886 4.0
-2.4568681261 1.9876969983 4.0
-4.9137362473 3.9753939959 4.0
-7.3706043669 5.9630909933 4.0
-9.8274724865 7.9507879906 4.0
0.4929619475 3.121558803 4.0
-1.9639061721 5.1092558003 4.0
-4.4207742933 7.0969527979 4.0
-6.8776424119 9.0846497965 4.0
3.442792021 4.2554206076 4.0
0.9859239015 6.2431176049 4.0
-1.4709442187 8.2308146037 4.0
-3.9278123383 10.2185116011 4.0
-6.3846804579 12.2062085984 4.0
3.9357539761 7.3769794108 4.0
1.4788858565 9.3646764081 4.0
-0.9779822647 11.3523734057 4.0
-3.4348503843 13.340070403 4.0
6.8855840496 8.5108412154 4.0
4.4287159301 10.4985382127 4.0
1.9718478089 12.4862352103 4.0
7.3785460036 11.6324000173 4.0

In this case, how can I set things like LDAUU as you have described?

Regards,
Zhao

[merzuk.kaltak]

Dear Zhao,

it depends on which ion species you want to apply a U-term.
For instance, setting a U-value of 3.2 for Mo for the POSCAR posted above this would be now

Code: Select all

LDAUU= 0 3.2 0 

To learn more about this method, I suggest to go through following DFT+U tutorial.

[hszhao.cn@gmail.com]

Dear merzuk.kaltak,

For instance, setting a U-value of 3.2 for Mo for the POSCAR posted above this would be now

In this format, how can I still set different subsets of the Mo atoms with different U-values?

[merzuk.kaltak]

Dear Zhao,
your question has been answered in one of my previous post.