DL-FIND constrained geometry optimization

[akhilshajan]

I have added DL-Find feature for constrained geometry optimization.

# Example input for DL-FIND constraint integration in QUICK
HF BASIS=3-21G CONSTRAIN OPTIMIZE

C         -4.13498124  0.70342204  0.00000000
H         -3.53650966  -0.16516720  -0.17967886
H         -4.07172084  1.36057017  -0.84205371
H         -5.15338585  0.41046458  0.14808100
C         -3.62163902  1.42937832  1.25740497
H         -3.68306794  2.48719615  1.10858318
H         -4.22133413  1.15219316  2.09909028
H         -2.60384227  1.15314360  1.43819258

DIHEDRAL 2 1 5 6

The syntax for implementing constraints within QUICK closely mirrors established conventions in other QM packages:

FREEZEXY atom_no_1
DISTANCE atom_no_1 atom_no_2
ANGLE atom_no_1 atom_no_2 atom_no_3
DIHEDRAL atom_no_1 atom_no_2 atom_no_3 atom_no_4

Commands such as DISTANCE, ANGLE, and DIHEDRAL enable straightforward specification of constraints, streamlining the optimization process. These constraints operate within the default internal coordinate system (ICOORD=3) of QUICK, simplifying the setup process for users familiar with similar packages.

The freeze atom commands (FREEZE, FREEZEX, FREEZEY, FREEZEZ, FREEZEXY, FREEZEXZ, FREEZEYZ) provide fine-grained control over molecular configurations, enhancing the precision and accuracy of simulations. The freeze atom functionality is compatible with Cartesian coordinate systems (ICOORD=0)of QUICK.

[Madu86]

@akhilshajan , I just tested this branch. Serial CPU and CUDA versions work fine; but not the MPI versions. Please check the attached zip file below.
ethane.zip

[Madu86]

Can you also add a test case to the test suite?

[akhilshajan]

Thank you Madu. I will check the error with MPI and add the test case with the test you tried out for constrained geometry optimization.

[Madu86]

Hi @akhilshajan, were you able to find this issue in the MPI version? Let me know if you need help.

[akhilshajan]

Hi @Madu86, thanks with the help for MPI. I have tested with CUDA and CUDA-MPI. It is working perfectly now. I believe we can merge this branch.

ethane.zip

[Madu86]

Thanks @akhilshajan. We will test this soon.

[dacase]

I've had less success here. I grabbed the code from [akhilshajan:QUICK_Constrained_Optimization], built and tested it with the sample input above (and other sample inputs). It never seems to recognize the CONSTRAIN keyword, just doing an unconstrained optimization.

I can be patient. Perhaps I'll wait until this PR is merged in, then try again. But just seeing if this rings any bells. (I don't have time or expertise to dig into the code at this point.)

...thanks...dac

[Madu86]

Hi Dave, It looks like the quick executable is using a shared object file from another installation. Can you please run ldd on quick executable and check if this is the case? Madu

…

On Nov 15, 2024, at 3:01 PM, David A Case ***@***.***> wrote: I've had less success here. I grabbed the code from [akhilshajan:QUICK_Constrained_Optimization], built and tested it with the sample input above (and other sample inputs). It never seems to recognize the CONSTRAIN keyword, just doing an unconstrained optimization. I can be patient. Perhaps I'll wait until this PR is merged in, then try again. But just seeing if this rings any bells. (I don't have time or expertise to dig into the code at this point.) ...thanks...dac — Reply to this email directly, view it on GitHub <#366 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALEIXIKQIEOJMYZM3UJ4BFD2AZHJNAVCNFSM6AAAAABHEGFSVSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZZHAZDONRXG4>. You are receiving this because you were mentioned.

[dacase]

You are right to some extent. I had to update my LD_LIBRARY_PATH (doesn't seem to be done via quick.rc(?) Now, ldd shows I am using /usr/local/lib/libquick_cuda.so instead of the one from Amber24. But the results are the same: the CONSTRAIN keyword is apparently not recognized. Probably I am still doing something wrong, but I don't see it.

[Madu86]

I still think this is a path issue. I have separate Amber24 and quick development (quick-const-opt) installations on my system.
This is what I compiled:

[madu@osprey quick-const-opt]$ git branch
* QUICK_Constrained_Optimization
[madu@osprey quick-const-opt]$ git log
commit 99797037c6309377b6f474bcc6bebbba78609cbf (HEAD -> QUICK_Constrained_Optimization, origin/QUICK_Constrained_Optimization)
Merge: 46ee0c15 1d6cf2d4
Author: Akhil Shajan <[email protected]>
Date:   Thu May 2 13:52:55 2024 -0400

    Merge branch 'merzlab:master' into QUICK_Constrained_Optimization

Running ldd on quick.cuda from Amber24 installation gives me this:

[madu@osprey bin]$ ldd /home/madu/Apps/amber24/install/bin/quick.cuda
	linux-vdso.so.1 (0x00007ffd9afb4000)
	libquick_cuda.so => /home/madu/Apps/amber24/install//lib/libquick_cuda.so (0x00007fe27e400000)

And this is from QUICK development installation:

[madu@osprey bin]$ ldd /home/madu/Apps/quick-const-opt/install/bin/quick.cuda 
	linux-vdso.so.1 (0x00007ffce49ce000)
	libquick_cuda.so => /home/madu/Apps/quick-const-opt/install//lib/libquick_cuda.so (0x00007f37c6c00000)

Ethane test:

. /home/madu/Apps/quick-const-opt/install/quick.rc 
quick.cuda ethane.in

I have attached my input and output below.
ethane-rtx3080ti.tar.gz

[dacase]

Ah...my fault. I had built from the master branch, and not from Quick_Constrained_Optimization. Thanks for your help; apologies for the noise. Everything now seems to work as I expected.

[Madu86]

No worries at all! Glad you figured it out and got everything working as expected. On Nov 15, 2024, at 6:56 PM, David A Case ***@***.***> wrote: Ah...my fault. I had built from the master branch, and not from Quick_Constrained_Optimization. Thanks for your help; apologies for the noise. Everything now seems to work as I expected. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>