code freeze Feb 25

[hainm]

@drroe AMBER code is due by Feb 15, can we (you) try to finish new features soon and try to finish created issues? I would like to freeze pytraj code this month (Jan) and would like to have stable cpptraj API.

[hainm]

it's up to you but there are few things I would like to have in cpptraj v16.

• supporting XTC format. #156
• updating doc (several issues)
• dump data to dataset rather stdout

and do you almost finish MPI stuff?

[drroe]

@hainm The only remaining API change I would like to get in are the changes in drroe/cpptraj/parallel_trajin, which I hope to have done soon (and I think these should be minor and may not even affect pytraj). I will try to address as many issues as I can before the code freeze, but I will probably be working right up to the Feb 15 deadline. However, I will not make any API changes after January in order to accommodate pytraj (unless it involves a code breaking bug or something).

[hainm]

Sounds good to me.

Hai

On Jan 4, 2016, at 10:31 AM, Daniel R. Roe notifications@github.com wrote:

@hainm The only remaining API change I would like to get in are the changes in drroe/cpptraj/parallel_trajin, which I hope to have done soon (and I think these should be minor and may not even affect pytraj). I will try to address as many issues as I can before the code freeze, but I will probably be working right up to the Feb 15 deadline. However, I will not make any API changes after January in order to accommodate pytraj (unless it involves a code breaking bug or something).

— Reply to this email directly or view it on GitHub.

[drroe]

@hainm The new code in my parallel_trajin branch is pretty much ready to go if you want to take it for a spin. I plan on merging either tomorrow or early next week.

[hainm]

Ok. I will test tonight.

Hai

On Jan 21, 2016, at 6:12 PM, Daniel R. Roe notifications@github.com wrote:

@hainm The new code in my parallel_trajin branch is pretty much ready to go if you want to take it for a spin. I plan on merging either tomorrow or early next week.

— Reply to this email directly or view it on GitHub.

[hainm]

@drroe

pytraj compile was stuck at

-    ActionFrame() : frm_(0) {}
-    ActionFrame(Frame* fIn) : frm_(fIn) {}
+    ActionFrame() : frm_(0), trajoutNum_(0) {}
+    ActionFrame(Frame* fIn, int t) : frm_(fIn), trajoutNum_(t) {}

Should I set trajoutNum_ = 0 (always) for in pytraj (use serial/openmp cpptraj)

[drroe]

For the blank constructor thats fine. In serial trajoutNum should be the same as frameNum (passed to DoAction()).

On Thursday, January 21, 2016, Hai Nguyen notifications@github.com wrote:

@drroe https://github.com/drroe

pytraj compile was stuck at

• ActionFrame() : frm_(0) {}
• ActionFrame(Frame* fIn) : frm_(fIn) {}
• ActionFrame() : frm(0), trajoutNum(0) {}
• ActionFrame(Frame* fIn, int t) : frm(fIn), trajoutNum(t) {}

Should I set trajoutNum_ = 0 (always) for serial cpptraj?

— Reply to this email directly or view it on GitHub https://github.com/Amber-MD/cpptraj/issues/215#issuecomment-173789634.

---

Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax)

[hainm]

thanks. tests failed, so I need a bit time to update pytraj's code.

[drroe]

Let me know if you need any help.