[CPMD-list] Metadynamics
Nora Mohamed
nora221282 at yahoo.com
Sun Feb 10 12:47:27 CET 2008
Hi CPMD users.
This is my first encounter with molecular dynamics and so I have few elementary question.
1. I am confused when to do bulk systems simulations and one molecule simulations. in the tutorials I read, I found examples that simulate only one water molecule and others that simulate many water molecules in the simulation cell. when I use either?
2. also, what does it mean when I have only one molecule in the simulation cell and have the SYMMETRY keyword is set to fcc or bcc. As I said this is my first encounter with simulation and so have a difficulty in imagining the supercell that is simulated.
3. If I wanted to enter the primitive cell vectors instead of the SYMMETRY keyword, do I still have to enter the atoms coordinates? wouldn't that be redundant since primitive vectors define the lattice completely?
4. I want to make sure of an information I read, is it right that in the &SYSTEM section, I define the symmetry and cell section according to the conventional cell and in the ATOMS section I put the atoms coordinates according to the primitive cell?
5. in the examples I read, I got confused by the way the atoms coordinates were defined. in some examples I find negative numbers like in the example below from Dr. Axel's website and from another tutorial I find the coordinates are defined from 0 to 1 or to the value of "scale". Are there any rules to use either or I have complete freedom in my choice.
&ATOMS
*O_VDB_BLYP.psp FORMATTED
LMAX=P
33
0.7327 -4.2440 2.1886
-0.8347 -4.7227 4.3691
2.6518 -1.5714 -0.1309
3.2623 -4.4641 2.6462
-4.7361 4.8510 -2.0459
-2.3920 0.3963 3.9231
-0.5493 -4.5740 -2.0499
2.2782 -3.3931 -4.3667
-3.5142 -4.3400 2.4342
-3.8442 0.5428 -2.4979
2.6625 2.2735 2.5634
4.0301 2.4810 -3.1204
-1.3385 -0.8110 -0.2060
3.3646 -4.3723 -0.2574
0.7415 -0.6233 -1.8793
4.5585 3.6260 4.3279
1.4453 3.8230 -1.3437
0.7650 1.2950 4.2396
-2.5713 3.1043 -4.8839
-4.1207 3.2564 1.0086
0.4496 3.1128 1.4121
4.0998 0.0228 4.2341
-0.5407 -2.4217 -3.9645
-4.5374 -1.1430 -0.2440
-1.6032 1.7664 0.5732
-3.1993 -1.5826 -4.4357
0.5592 -1.4779 1.7951
-1.8413 2.8694 -2.0738
0.9314 1.6635 -3.0237
4.8851 0.6455 1.8791
-4.7775 -3.9950 -4.5931
-2.9360 -3.2201 -0.0728
1.8651 -1.3161 4.1881
*H_VDB_BLYP.psp FORMATTED
LMAX=P
67
0.1804 -4.3091 3.0196
0.4583 -3.4352 1.6684
-0.8907 -3.8505 4.8551
-1.4470 -5.3849 4.8012
2.6813 -2.5699 -0.0836
3.5705 -1.2189 -0.3089
2.2641 -4.5114 2.6070
3.6143 -5.2567 3.1440
-5.2043 3.9908 -2.2480
-5.2257 5.3344 -1.3202
-2.8338 0.3816 3.0261
-2.6987 -0.3905 4.4587
0.2035 -5.0868 -1.6374
-1.2460 -5.2114 -2.3791
3.1464 -3.8096 -4.0969
1.5234 -3.8864 -3.9344
-4.2719 -3.7659 2.7445
-2.7608 -4.2804 3.0891
-3.5930 -0.0389 -3.2716
-3.0803 1.1482 -2.2743
3.3247 1.5747 2.2926
3.0265 2.7969 3.3338
4.7065 1.8430 -2.7522
3.1319 2.0416 -3.1370
-1.9556 -1.5794 -0.0367
-1.7355 0.0251 0.1726
3.1616 -4.3000 0.7191
2.7360 -5.0244 -0.6811
1.5443 -1.0463 -1.4591
-0.0408 -0.7072 -1.2621
5.5462 3.4712 4.3092
4.1734 3.2213 5.1573
1.3289 3.2796 -0.5124
1.3588 3.2301 -2.1443
1.2158 1.6650 3.4272
-0.2192 1.4615 4.1796
-2.3393 2.1786 -5.1828
-2.3958 3.1917 -3.9033
-4.0469 3.9980 1.6755
-4.8820 3.4416 0.3872
1.3081 2.8588 1.8577
0.2815 4.0896 1.5449
4.4722 0.2911 3.3456
4.8505 -0.1433 4.8736
-0.5906 -3.0520 -3.1897
-0.0056 -1.6175 -3.7060
-4.2505 -0.6992 -1.0929
-3.9724 -1.9523 -0.0834
-2.3879 2.3426 0.8019
-0.7686 2.1804 0.9365
-3.8725 -2.3207 -4.3898
-2.2782 -1.9717 -4.4453
1.3775 -1.3132 1.2443
-0.2523 -1.2143 1.2736
-1.1466 2.2371 -2.4168
-2.0815 2.6232 -1.1348
1.0048 0.8099 -2.5081
0.8075 1.4570 -3.9943
5.3467 1.4906 1.6095
4.9527 -0.0223 1.1379
-4.4389 -4.2859 -3.6983
-5.0180 -4.7996 -5.1361
-2.9873 -3.6787 0.8143
-2.9264 -3.9045 -0.8018
1.8677 -2.1810 4.7284
2.7693 -0.8629 4.0578
1.2248 -1.2816 3.3950
&END
6. In the example below ( from the Institute of Physical Chemistry (Group of Prof. Dr. Jürg Hutter), I found the information given in the SYSTEM section inconsistent with that given in the ATOMS sections which shows that there must be some information that I am missing. In the SYSTEM section I have the symmetry set to fcc and the cell size to 20.53 au and scale to 2 which is consistent with the information given in kittel (5th edition). according to Kittel p25 the silicon crystallizes in (diamond structure) an fcc lattice with two silicon atoms for the basis with conventional cell lattice constant a= 5.43 A = 10.263102 au half the value given under the CELL keyword. however, according to kittel p16 and p17 the primitive cell as shown takes up only one fourth of the volume of the conventional cell, and in the ATOMS section the primitive cell takes up the whole volume of the conventional cell. there must be something I am missing but I don't know what it is. Any help?
&SYSTEM
SYMMETRY
FCC
SCALE S=2
CELL
20.526204 1.0 1.0 0 0 0
CUTOFF
8.0
&END
&ATOMS
*Si_MT_LDA.psp KLEINMAN-BYLANDER
LMAX=P
16
0.00 0.00 0.00
0.25 0.25 0.25
1.00 0.00 0.00
1.25 0.25 0.25
0.00 1.00 0.00
0.25 1.25 0.25
1.00 1.00 0.00
1.25 1.25 0.25
0.00 0.00 1.00
0.25 0.25 1.25
1.00 0.00 1.00
1.25 0.25 1.25
0.00 1.00 1.00
0.25 1.25 1.25
1.00 1.00 1.00
1.25 1.25 1.25
&END
7. How to choose my pseudopotential? I know I have to test each pseudopotential for each atom in my simulation. for example if I am simulating ch4, then I have to test the pseudopotential for hydrogen alone and the pseudopotential for carbon alone. however, should I test the pseudopotential with bulk carbon or with one carbon molecule. I also want to know what the pseudopotential accuracy depends on. does it depend on my system (i.e my computer, operating system and the set up in general? I got that impression since I read everywhere that I must test the pseudopotential first)
8. I got warned that cf4 is a molecular crystal, bonded by Van der Waals forces between the molecules and so not well given by present Density Functional Theory calculations.Does this mean that I can't use cpmd to simulate cf4 or ch4 since my results would be wrong or inaccurate at best?
9. I also read that when I do calculations under high pressure, I must also watch that I do not have too much overlap between the pseudising spheres of neighboring atoms and that 10 percent maybe OK.Does anybody know how do I know that my pseudising spheres overlapped or even how to calculate that ten percent? I need more details on that matter please.
10. I am really worried about the results I get. I know I have to optimize my wavefunction at first and then do whatever molecular dynamics I need. the problem is how to know that my results are right; I mean is there any convention or procedure I should follow to make sure that the results I got, either from wavefunction optimization or molecular dynamics, are accurate? what values I should keep an eye on to validate my results or know that there is something wrong?
11. concerning Metadynamics, I don't know how to set the necessary parameters. Mainly I want to study how a material undergoes phase change under high pressure, I studied the example about silicon and read the section about metadynamics in the cpmd manual, but I think I should read more about this part. does anybody know any paper or material to read concerning this part or its theoretical background?
Thank you.
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