The ABINIT Users Mailing List ( CLOSED )

[paul.boulanger@umontreal.ca]

Hi Denes (and Hi Mikami),

                  The system considered is very interesting. Visualizing it 
using the program Jmol is very instructive. We first see that the system 
resembles two binuclear metallocenes linked together by an iodine and copper 
complex. We first see that the carbon rings of the metallocene like 
structures are passivated by CH3. Usually, to minimize the numbers of atoms 
we can replace CH3 by H only, which diminishes the number of atoms by 60 in 
your case. This permutation does not change the electronic properties too 
much; usually the effect on binuclear metallocenes is to change a little the 
strength of the bond between the metal atoms. Just keep this in mind. I think 
reducing the number of atoms be half can be worth it.

            Another point, that can be important before relaxing your system, 
is to inspect the geometries of every site. We see that the bond between the 
Cu and P at one of your Mo site seems a little strange, considering the other 
sites. Maybe manual cleaning will help the convergence of the relaxation and 
of the SCF.

                  You will find at the end of this reply the content of the 
.xyz file used to visualize your system. It will work directly with Jmol, if 
you copy the ASCII data in file and name it filename.xyz. The atomic 
positions are in angstroms.

                                                        Have a nice day,
                                                                     paul

###########################forum.xyz file ####################
120
angstrom
Mo              2.1235117804             -4.7988253114              
2.6457073552
Mo               1.69725115             -5.6385747374              
5.4112152562
Mo              6.3740896804              2.4677074332              
5.3679468869
Mo              3.8801464024              2.3997284697              
4.9043598097
P               5.987273546              0.3593647506              
4.9674557322
P              5.7623532276              3.0460418207              
3.0058897479
P              4.6645067072              4.6008730962              
4.2497963547
P              4.1438285236               3.018866026              
7.0218226546
P              3.8078892872             -4.9700280808              
4.1075536333
P              0.7680623592             -3.0722859641              
4.2802458114
P             -0.2576137372             -4.5092554548              
4.0772131192
P              1.7820568164             -7.1265166077              
3.7697044736
S              3.9167951072             -7.1095258145              
3.8285697918
S              4.9952661444              0.7356729223              
7.0932345289
C              2.7779436492             -3.1905898885              
0.6538916423
C               3.710816816             -4.6059577016               
0.517658921
C              2.8488787236              -5.466266619              
0.4216986475
C              1.3856179588             -4.5912565599              
0.5011178029
C              1.3357921916             -3.1942059588              
0.6731018541
C              3.2110528844             -1.8962104188               
0.683433244
C              5.3234031728             -5.1009487745              
0.4091157772
C              3.4032472748             -6.9865636336              
0.1490153197
C              0.1460421628             -5.0266377403              
0.3335096128
C              0.0228214584             -1.9173383754                
0.72083687
C               2.589466144             -6.6583381434              
7.5303303972
C              1.8321860028             -7.5576974619              
7.3061446835
C                0.34513934             -6.7571405533              
7.3452006056
C              0.1935489404              -5.344520322              
7.5676250806
C               1.576208562             -5.2876422206              
7.6886058379
C               4.133165506             -7.1425283775              
7.7293685274
C              2.4812213444             -9.1257929254              
7.2151049841
C              -0.829851512             -7.3299008237              
7.2319547729
C             -1.1809617084             -4.1475694713              
7.7708030296
C              1.8801587456             -4.0459878982              
8.0382389555
C              8.8733753036              2.0486380459              
4.6609820413
C              8.6199010712              1.3111965652              
6.0638540586
C              7.8493788492              2.3612939059              
6.9382818375
C              7.6257047168              3.7502122965              
6.0733502219
C              8.2418732572              3.5540444304              
4.6689530082
C              9.7367438008              1.3697642715              
3.4111017486
C              9.1611250692             -0.2866959492              
6.5669328283
C              7.4482803396              2.0574650472              
8.5004097789
C              6.9294660168               5.171927971              
6.5685488102
C              8.3326714528              4.7377468838              
3.4212697246
C              1.9886636188              3.4946240263              
3.6191276433
C               2.588761778              2.0386425328              
3.3911652528
C              2.3553890676              1.1172551878              
4.7000924347
C              1.6050117132               2.003050295              
5.7315791286
C              1.3654514184              3.4624741611              
5.0723492989
C               1.894961268              4.8352544563              
2.5219304045
C              3.2486877016              1.5784699534              
1.9915433564
C              2.7095009468             -0.5020179344              
4.9248773327
C              1.0459618372              1.4852890327              
7.2442108154
C              0.4843220616               4.766580702              
5.7231723913
H               3.364106198             -1.3602898515             
-0.2678353821
H              4.1019783468             -2.2063555575              
1.0688721628
H              2.4496982568             -1.2773570951              
1.2685457915
H              5.6083463108             -6.0184516073              
1.0411644282
H              5.6382547748             -4.3803875521              
0.6681449658
H              5.7706647464             -5.2253794905             
-0.5524842388
H              3.8206762392             -6.9842108193             
-0.8402016454
H              2.6099035944             -7.4181076739              
0.3864375593
H              4.1400357836             -7.5470229487              
0.7232880785
H               0.141848476             -4.9434523327             
-0.6619533947
H              -0.753509074             -4.3972520197              
0.7540280488
H              0.2379565076             -6.0243573291              
0.7986945148
H             -0.0729072992             -1.3942082751             
-0.2296328437
H              0.1140314372             -1.2805468165              
1.2825086014
H             -0.8290821276             -2.2443479817               
1.140810593
H              4.4443977504              -6.302384184              
7.7027320617
H              4.7333720292              -7.661331826              
6.9809147083
H              4.2270845848             -7.7792094015              
8.6340823491
H               2.731802258             -9.6665770283              
8.1207992892
H               3.348501782              -9.249560432              
6.5015672683
H              1.7863480308             -9.4831838385               
6.963610992
H              -0.501400228             -7.8896811387               
6.473914005
H             -1.6784174868              -6.526454217              
7.0345326246
H             -1.0764988124             -7.9473329844              
8.1135182921
H             -1.4927357728             -4.1045240231              
8.7679728045
H             -1.9252273332             -4.3281361258              
7.4100577668
H             -1.0189900376             -3.2315035922              
7.2665622055
H              1.7486048496             -4.1377160745              
9.0546189422
H               1.218661544             -3.1427598582              
7.6583924235
H              2.8713967628             -4.0478196194              
7.6296860484
H             10.7192801888              1.4371747698               
3.249031474
H               9.292375546              1.8751298343              
2.5854620974
H              9.7584274372              0.3568066572              
3.5883513588
H             10.1249144852             -0.5230195654              
6.7903014725
H              9.1990307964             -0.8030834206               
5.832968375
H              8.5108110324             -0.5713864795              
7.4041567093
H              8.2692134944              1.9651052429              
8.9282818404
H              7.1793750736              1.1600479848              
8.7830431975
H              6.6346292456              2.8490686289              
8.8087899653
H              7.6697546828              5.5279135118               
6.734831532
H              6.2528628736              5.0442443708              
7.4377836585
H              6.4134366488              5.8673188176              
5.8547750521
H               7.534169646              5.6004717783              
3.5772392136
H              8.2775683588              4.4235909073              
2.5837916442
H              9.2451396784              4.9565744044              
3.2939158252
H              2.4308429208              4.5721498129              
1.6227908125
H               2.306473558              5.4761200158               
2.792925122
H               0.886742612              5.3277505986              
2.4378630315
H              2.5086374364              1.4505968648              
1.5812292106
H              4.0109959324              0.6685940287              
2.1168273464
H              3.6545108816              2.3177115739              
1.3687003551
H              1.8558310276             -0.7683122992              
4.9033611692
H                 3.0179374             -0.9168238327              
5.8332588886
H              3.4842060192             -0.8703044305              
4.1836863536
H              1.2252284024              2.0358159975              
7.8404355081
H              1.5395165116              0.4626833007              
7.5061996113
H              0.0114649112              1.6224312622              
7.3645560742
H             -0.5090290536              5.0316591829              
5.5683831138
H              0.8879996344              5.5694746342              
5.2948464023
H              0.5024405224              4.5445792507              
6.7284402328
Cu              8.3929326732             -4.4676153789              
3.8999816661
Cu              5.9834157876             -4.9889295487               
4.286709739
Cu              6.5284325256             -1.8695872986              
4.6078362096
I                8.30908061             -6.9715150965              
3.6174208759
I               6.858195014             -2.4002811442              
2.1541038727
I               6.196578612             -4.0162382194              
6.4924160899
################################end of file##############################