关注：

1） 一些悬而未决的问题，如声子谱虚频处理

2）Ramma及红外光谱计算

3） 介电函数及功函数的计算

4） 过渡态搜索

5)   STM模拟

hi there Xiaoqiu
Roald just told me you're back in China.

Sichuan is a long love of mine, for the cuisine - I love spicy and hot! hope to see S. one day (I have one friend, now in Beijing, who originated from there)...

re: phonons. you may do it using VASP without having phonon, but ONLY if your imaginary mode is in the zone 【地带】center.

      I discovered it 3 days ago. the following scheme applies.
1. you do optimization and then calculate phonons at zone center with vasp【zone  center是否就是gamma点？】

2. if there are any img freq vasp lists their frequencies as f/i, not f. aside from translations which are +/- 0 cm-1, you may find true imaginary mode.

3. if this is the case, go to phonon OUTCAR, not normal outcar, but phonon one. h

here you find the entire matrix of atomic motions related to each phonon, in Cartesian coordinates. the cell is also listed in cartesian coordinates.  【注意是笛卡尔坐标】
so for each atomic coordinate, x, you apply: x'=x0+x_displ

where x0 is its initial coordinate in the cell and x_displ is the lissted cartesian coordinate.
when you have obtained new Cartesian coordinate positions, you may express them in fractional coordinates of the unit cell, in order to have new cif. which you subsequently optimize.
good luck & best
w
----- Oryginalna wiadomość -----
Od: xiaoqiugood@sina.com
Do: "w.grochala" <w.grochala@cent.uw.edu.pl>
DW: "rh34" <rh34@cornell.edu>
Wysłane: wtorek, 22 lipiec 2014 2:34:44
Temat: Questions and greetings from Xiaoqiu
Dear Prof. Wojciech Grochala,
First of all, I hope everything goes very well with you.
Thank you very much for your concern.
Yes, how to follow img phonon still puzzles me. In my work, I find the Gd H 3 structure for ScH 3 is not dynamically stable from 1 atm to 25 GPa, as shown in the attached file.
Could you kindly tell me how to follow the corresponding eigenvector ( or the imaginary phonon vectors) to a more stable minimum ? You can find the 'cif' file and the result of phonon calculations of ScH 3 in the attachment.
Thank you very much for your time and looking forward to your kindly suggestions.
Best wishes,
Sincerely yours,
Xiaoqi

笛卡尔坐标

顾名思义，前者是定义在三个晶矢方向上的坐标
R=R1×x+R2×y+R3×z R1,R2,R3为前面的晶矢，x,y,z为输入的三个坐标，R为坐标位矢
而后者只是简单的将直角坐标除以前面第二行定义的晶胞常数

可以混用，但不推荐。

笛卡尔坐标(基于坐标系)与直接坐标(基于基矢，即将基矢当坐标系)/分数坐标

原子位置为Driect坐标的POSCAR

sch3-d194ph-reopt800ev-at-0G
1.0
       3.3631999493         0.0000000000         0.0000000000
      -1.6815999746         2.9126165941         0.0000000000
       0.0000000000         0.0000000000         6.1085000038
   H   Sc
   6    2
Direct
    0.333333343         0.666666687         0.592360020
    0.666666627         0.333333313         0.407639980
    0.666666627         0.333333313         0.092360020
    0.333333343         0.666666687         0.907639980
    0.000000000         0.000000000         0.750000000
    0.000000000         0.000000000         0.250000000
    0.666666687         0.333333343         0.750000000
    0.333333313         0.666666627         0.250000000

原子位置为笛卡尔坐标的POSCAR

sch3-d194ph-reopt800ev-at-0G
1.0
       3.3631999493         0.0000000000         0.0000000000
      -1.6815999746         2.9126165941         0.0000000000
       0.0000000000         0.0000000000         6.1085000038
   H   Sc
   6    2
Cartesian
    0.000000000         1.941744454         3.618431182
    1.681599874         0.970872140         2.490068821
    1.681599874         0.970872140         0.564181181
    0.000000000         1.941744454         5.544318823
    0.000000000         0.000000000         4.581375003
    0.000000000         0.000000000         1.527125001
    1.681600025         0.970872227         4.581375003
    0.000000000         1.941744280         1.527125001

Eigenvectors and eigenvalues of the dynamical matrix【笛卡尔坐标，谁是特征值，谁是特征矢量？】
----------------------------------------------------
 
 
  1 f  =   45.330845 THz   284.822099 2PiTHz 1512.074180 cm-1   187.473372 meV
            X         Y         Z           dx          dy          dz
     0.680334  2.512326 -3.157993     0.009095    0.015221    0.006861  
    -1.941439  1.188186 -4.776220    -0.013008   -0.014109    0.008459  
    -4.563213 -0.135953 -6.394447     0.003913   -0.001112   -0.015321  
     0.682060  5.766764 -2.349084     0.003913   -0.001112   -0.015321  

/////

获得笛卡尔坐标的POSCAR优化完毕后自动产生direct的POSCAR和CONTCAR
    -1.939714  4.442624 -3.967311     0.009095    0.015221    0.006861  

.....

LATTYP: Found a hexagonal cell.
ALAT       =    10.0475136129
C/A-ratio  =     0.6102071285
 
 Lattice vectors:
 
A1 = (  -7.8552591807,  -3.9673379546,  -4.8484711661)
A2 = (   0.0051684581,   9.7508240773,   2.4236219507)
A3 = (   2.6410880508,   1.3333414029,  -5.3699912156)
Subroutine PRICEL returns following result:
 
 LATTYP: Found a hexagonal cell.
ALAT       =     5.8009353121
C/A-ratio  =     1.0569096361
 
 Lattice vectors:
 
A1 = (   2.6149740626,  -5.1781039947,   0.0004090122)
A2 = (   2.6201425207,   4.5727200826,   2.4240309629)
A3 = (  -2.6410880508,  -1.3333414029,   5.3699912156)
 
  3 primitive cells build up your supercell.
 

Analysis of symmetry for initial positions (statically):

Routine SETGRP: Setting up the symmetry group for a
hexagonal supercell.

.....

energy-cutoff  :      400.00
 volume of cell :      536.02
     direct lattice vectors                 reciprocal lattice vectors
   -7.855259181 -3.967337955 -4.848471166    -0.103714419  0.011993420 -0.048031287
    0.005168458  9.750824077  2.423621951    -0.051806017  0.102584910 -0.000008109
    2.641088051  1.333341403 -5.369991216     0.070260481  0.035470689 -0.142857095

 length of vectors
   10.047514115 10.047514133  6.131064430     0.114924007  0.114924006  0.163103815

..........

position of ions in fractional coordinates (direct lattice)
  0.09710362  0.20532927  0.58500452
  0.46133740  0.22510789  0.58500461
  0.77489210  0.23622969  0.58500452
  0.12800408  0.55844127  0.58500464
  0.44155877  0.56956296  0.58500451
  0.76377024  0.53866263  0.58500449
  0.10822545  0.90289634  0.58500453
  0.43043691  0.87199591  0.58500448
  0.79467079  0.89177458  0.58500450
  0.23626563  0.12788831  0.08500871
  0.55828949  0.09706766  0.08500863
  0.87211171  0.10837718  0.08500854

.......

position of ions in cartesian coordinates  (Angst):
  0.78333557  2.39689749 -3.11463273
 -2.07771270  1.14471692 -4.83267430
 -4.54070892  0.00918604 -6.32597969
  0.54242982  5.71743800 -2.40864333
 -1.92056640  4.58190612 -3.90194872
 -4.45178079  3.00228062 -5.53907239
  0.69957612  9.15462720 -1.47791776
 -1.83163827  7.57500070 -3.11504143
 -4.69268755  6.32282013 -4.83308298

.....

网络摘录：表面slab模型在vasp里的POSCAR输入

http://leiustc.blog.sohu.com/82884774.html

有两种输入方式，一是Cartesian方式，二是Direct方式。

1. Cartesian坐标系的xy平面需与所建立平面平行，Z轴方向则垂直于所建立平面【即建立的表面？！】。

2. Cartesian方式与基矢无关。通过基矢反推出坐标系【尽管对于立方晶系，二者趋于一致，但基矢不同于坐标系，】的方向后，再以坐标系直接写出Cartesian坐标。

3. Direct方式是基于基矢的。故而它的方式是从基矢出发，再给出原子坐标的值，即基矢为Direct方式的坐标系。

FCC 三个特殊方向的POSCAR输入方式：

AL(100)(1x1)
3.97
 .50  0.5 0.0
-0.5  0.5 0.0
 0.0  0.0 5.0
   5
Cartesian
0.00 0.00 0.00
0.00 0.50 0.50
0.00 0.00 1.00
0.00 0.50 1.50
0.00 0.00 2.00
#end
#form OUTCAR
position of ions in fractional coordinates (direct lattice)
  0.00000000  0.00000000  0.00000000
  0.50000000  0.50000000  0.10000000
  0.00000000  0.00000000  0.20000000
  0.50000000  0.50000000  0.30000000
  0.00000000  0.00000000  0.40000000

position of ions in cartesian coordinates  (Angst):
  0.00000000  0.00000000  0.00000000
  0.00000000  1.98500000  1.98500000
  0.00000000  0.00000000  3.97000000
  0.00000000  1.98500000  5.95500000
  0.00000000  0.00000000  7.94000000

AL(110)(1x1)
3.97
 .707107  0.0 0.0
 0.0  1.0 0.0
 0.0  0.0 4.242641
   5
Direct
0.00 0.00 0.00
0.50 0.50 0.0833333333
0.00 0.00 0.1666666667
0.50 0.50 0.25
0.00 0.00 0.3333333333
#end  
#from OUTCAR
position of ions in fractional coordinates (direct lattice)
  0.00000000  0.00000000  0.00000000
  0.50000000  0.50000000  0.08333333
  0.00000000  0.00000000  0.16666667
  0.50000000  0.50000000  0.25000000
  0.00000000  0.00000000  0.33333333

position of ions in cartesian coordinates  (Angst):
  0.00000000  0.00000000  0.00000000
  1.40360740  1.98500000  1.40360706
  0.00000000  0.00000000  2.80721413
  1.40360740  1.98500000  4.21082119
  0.00000000  0.00000000  5.61442826

AL(111)(1x1)
3.97
 .707106   0.0 0.0
-0.353553  0.612372 0.0
 0.0  0.0  5.1961524
   5
Direct
0.0     0.0       0.0
0.33333 0.66667   0.11111
0.66667 0.33333   0.22222
0.00000 0.00000   0.33333
0.33333 0.66667   0.44444
#end
#from OUTCAR
position of ions in fractional coordinates (direct lattice)
  0.00000000  0.00000000  0.00000000
  0.33333000  0.66667000  0.11111000
  0.66667000  0.33333000  0.22222000
  0.00000000  0.00000000  0.33333000
  0.33333000  0.66667000  0.44444000

position of ions in cartesian coordinates  (Angst):
  0.00000000  0.00000000  0.00000000
 -0.00001404  1.62075266  2.29205764
  1.40361945  0.81036418  4.58411528
  0.00000000  0.00000000  6.87617291
 -0.00001404  1.62075266  9.16823055