qijingzheng / hefei-namd Goto Github PK

Mabe, it would be easier to read and modify the code if there is a more detailed explanation about the architecture of the source code. A simple diagram would be enough.
For example, if I wanna know the difference between namd, namdk and dish, maybe there should be a list of reference literature.

您好，按照文档中的方法编译运行后报段错误，更换了多个软硬件平台还是有问题，麻烦您帮忙看下，谢谢！

In the "couplings.f90":
315 close(unit=23)
316 close(unit=23)

It seems that either of them should be changed to "unit=22".

The similar issue exists in the bottom part of this file.
346 close(unit=23)
347 close(unit=23)

Dear Dr. Zheng,

The formula for non-adiabatic coupling terms is

d_{ij} = (<psi_i(t)|psi_j(t+dt)> - <psi_i(t+dt)|psi_j(t)>) / (2dt)

according to Prezhdo's paper (doi: 10.1021/ct400641n) and pp. 19 of your PhD dissertation. However, in the documentation of CoupIJ of coupling.f90, it is

! <psi_i(t)|psi_j(t+dt)>
pij = SUM(CONJG(crA(:,i)) * crB(:,j))

! <psi_j(t)|psi_i(t+dt)>
pji = SUM(CONJG(crB(:,i)) * crA(:,j))

Since crA and crB are wave functions at t and t+dt respectively, the documentation has missed a conjugate term * at the end of the braket. It should be <psi_j(t)|psi_i(t+dt)>* or <psi_i(t+dt)|psi_j(t)>. The source code, on the contrary , is right.

While running the tdks.py code, the code gives an error: