Gaussian Hessian format

[YuraM]

Good afternoon,
at the end of the Gaussian/Priroda frequency job we have the second derivative matrix, like this is for water:

-0.01195539,0.,0.66747609,0.,0.,0.44764291,0.00597770,0.,0.,-0.00487871,0.
,-0.33373804,-0.20571172,0.,0.36413570,0.,-0.26668576,-0.22382146,0.,0
.23619874,0.21477179,0.00597770,0.,0.,-0.00109899,0.,0.,-0.00487871,0.
,-0.33373804,0.20571172,0.,-0.03039766,0.03048702,0.,0.36413570,0.,0.2
6668576,-0.22382146,0.,-0.03048702,0.00904966,0.,-0.23619874,0.21477179

I have a few questions:
1) Do I understand correctly that these are in Hartree/bohr**2?
2) What is the format of the output? Imagine we have molecule of water
x1 y1 z1
x2 y2 z2
x3 y3 z3

What is the sequence in this 1d array of the second derivatives(Hessian)?
Is it like: dx1dx1, dx1dy1, dx1dz1, dx1dx2.....

Just really got confused.

Thank you!

[madschumacher]

Не знаю как в Природе, но в Gaussian -- нижний треуголниk Гессиана построчечно.
Т.е. нижняя часть Гессиана будет уложена в следующей последовательности:

Код: Выделить всё

  F[x1x1] (1)
  F[y1x1] (2)  F[y1y1] (3)
  F[z1x1] (4)  F[z1y1] (5)  F[z1z1] (6)
  F[x2x1] (7)  F[x2y1] (8)  F[x2z1] (9)  F[x2x2] (10) 
  ..............................................................................................
  ..............................................................................F[yNyN] (3N*(3N+1)/2 - 3N)
  F[zNx1] (3N*(3N+1)/2-3N+1)............................................................. F[zNzN] (3N*(3N+1)/2)

где F[ab] = d²V/(da db), а номер в kруглых ckобkах -- это номер данной цихФерkи в строчечной записи Гессиана (т.е. в kусkе после Nimag в log-е Gaussian-a).

[madschumacher]

изначальный ответ был неверный, предыдущее сообщение изменено, чтобы соответствовать действительности.
А единицы, да -- Хартри/Бор²

А в kачестве примера -- Гессиан для Br₂ из выдачи Гауссиана:
[cut]6186361\PolarDeriv=0.,0.,0.,6.6948459,0.,0.,0.,0.,0.,0.,6.6948459,0.,0
.7826308,0.,0.7826308,0.,0.,19.8575786,0.,0.,0.,-6.6948459,0.,0.,0.,0.
,0.,0.,-6.6948459,0.,-0.7826308,0.,-0.7826308,0.,0.,-19.8575786\Quadru
pole=-1.30967,-1.30967,2.61934,0.,0.,0.\QuadrupoleDeriv=0.,0.,0.,0.,0.
8908694,0.,0.,0.,0.,0.,0.,0.8908694,-0.5540021,-0.5540021,1.1080042,0.
,0.,0.,0.,0.,0.,0.,-0.8908694,0.,0.,0.,0.,0.,0.,-0.8908694,0.5540021,0
.5540021,-1.1080042,0.,0.,0.\PG=D*H [C*(Br1.Br1)]\NImag=0\\0.00001939,
0.,0.00001939,0.,0.,0.13566840,-0.00001939,0.,0.,0.00001939,0.,-0.0000
1939,0.,0.,0.00001939,0.,0.,-0.13566840,0.,0.,0.13566839\\0.,0.,0.0000
0215,0.,0.,-0.00000215\\0.,0.,0.,0.,0.03042640,0.,0.03042640,0.,0.,-0.
33468663,0.,0.,0.,-0.03042639,0.,0.,0.,0.,0.03042641,0.,0.,0.,0.,0.,-0
.03042639,0.,0.,0.,0.,0.,0.,0.,0.03042641,0.,0.,-0.03042641,0.,-0.0304
2641,0.,0.,0.33468655,0.03042639,0.,0.,-0.03042640,0.,0.03042639,0.,0.
,-0.03042640,0.,0.,-0.33468655,0.,0.,0.33468663\\@[/cut]

И этот же kусоk, преобразованный в нижне-треугольный вид:
[cut]

Код: Выделить всё

  Br1x   1.939000e-005
  Br1y   0.000000e+000  1.939000e-005
  Br1z   0.000000e+000  0.000000e+000  1.356684e-001
  Br2x  -1.939000e-005  0.000000e+000  0.000000e+000  1.939000e-005
  Br2y   0.000000e+000 -1.939000e-005  0.000000e+000  0.000000e+000  1.939000e-005
  Br2z   0.000000e+000  0.000000e+000 -1.356684e-001  0.000000e+000  0.000000e+000  1.356684e-001
           Br1x           Br1y           Br1z           Br2x           Br2y           Br2z           

[/cut]

[YuraM]

Spasibo za bystryi otvet i popravky!

[YuraM]

Yesterday spent half of a day to understand the format of Gaussian...

[madschumacher]

No problem

Если нужно, то могу скинуть конвертирующие программы для Гессиана (не свои).

[YuraM]

Thanks, I wrote a monkey code for that, google helped me to map 1d array onto lower triangular matrix, it works somehow.

[madschumacher]

А, ну это тоже хорошо и полезно! Тогда удачи с этим)