AttributeError for geometric_solver

[xptree]

###job_id=966###
smi: CC1C2C3CC4C(C3)C22CC14C=C2
xyz: 
C          0.56227       -0.19715        0.02741
C          0.66276        1.33457        0.43026
C         -0.04104        1.51621        1.74897
C         -0.44437        3.03446        2.17839
C          0.71581        4.03070        2.68997
C          1.84667        3.89880        1.58133
C          0.97410        3.38738        0.59886
C         -0.51016        3.69182        0.82971
C          1.39869        1.67823        1.56970
C          2.37946        1.93824        2.61169
C          2.26553        2.43369        1.15684
C          3.41182        1.90065        0.42822
C          2.79022        0.79292        0.76093
H         -0.48044       -0.42187       -0.22926
H          0.83412       -0.88156        0.83969
H          1.16561       -0.41261       -0.86129
H          0.22457        1.78675       -0.48672
H         -0.22964        0.71014        2.45798
H         -1.37674        3.09543        2.74257
H          1.03004        3.85624        3.72077
H          0.33898        5.06470        2.69063
H          2.45375        4.75901        1.30742
H          1.30691        3.47238       -0.45940
H         -1.19950        3.19202        0.14262
H         -0.73747        4.76305        0.82866
H          1.84387        2.22584        3.50693
H          3.01542        1.08864        2.89202
H          4.40346        2.14521        0.11562
H          3.07262       -0.24616        0.81319

Traceback (most recent call last):
  File "/root/anaconda3/bin/dispynode.py", line 208, in _dispy_job_func
    __dispy_job_name, globals(), localvars)
  File "<string>", line 1, in <module>
  File "<string>", line 18, in compute
  File "./pyscf_geomopt.py", line 99, in hfsto3g
    mol_sto3g = optimize(mf, grad_cb)
  File "./pyscf_geomopt.py", line 64, in optimize
    opt.kernel()
  File "/root/pyscf/pyscf/geomopt/geometric_solver.py", line 171, in kernel
    maxsteps=self.max_cycle, **self.params)
  File "/root/pyscf/pyscf/geomopt/geometric_solver.py", line 119, in kernel
    constraints=constraints, **kwargs)
  File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 1708, in run_optimizer
    progress = Optimize(coords, M, IC, engine, dirname, params, xyzout)
  File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 1300, in Optimize
    return optimizer.optimizeGeometry()
  File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 1265, in optimizeGeometry
    self.step()
  File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 1076, in step
    self.checkCoordinateSystem(recover=True, cartesian=LastForce)
  File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 946, in checkCoordinateSystem
    if self.IC.repr_diff(IC1) != "":
  File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/internal.py", line 3021, in repr_diff
    return self.Prims.repr_diff(other.Prims)
AttributeError: 'CartesianCoordinates' object has no attribute 'Prims'

[gkc1000]

Assuming this is not an input error, this error is occurring in the external "geometric" library which is maintained by the developers here: https://github.com/leeping/geomeTRIC However, to diagnose this problem, you need to post the full pyscf input, not just the traceback. As an alternative, you can try using the berny solver.

…

On Wed, Mar 13, 2019 at 2:22 AM Jiezhong Qiu ***@***.***> wrote: ###job_id=966### smi: CC1C2C3CC4C(C3)C22CC14C=C2 xyz: C 0.56227 -0.19715 0.02741 C 0.66276 1.33457 0.43026 C -0.04104 1.51621 1.74897 C -0.44437 3.03446 2.17839 C 0.71581 4.03070 2.68997 C 1.84667 3.89880 1.58133 C 0.97410 3.38738 0.59886 C -0.51016 3.69182 0.82971 C 1.39869 1.67823 1.56970 C 2.37946 1.93824 2.61169 C 2.26553 2.43369 1.15684 C 3.41182 1.90065 0.42822 C 2.79022 0.79292 0.76093 H -0.48044 -0.42187 -0.22926 H 0.83412 -0.88156 0.83969 H 1.16561 -0.41261 -0.86129 H 0.22457 1.78675 -0.48672 H -0.22964 0.71014 2.45798 H -1.37674 3.09543 2.74257 H 1.03004 3.85624 3.72077 H 0.33898 5.06470 2.69063 H 2.45375 4.75901 1.30742 H 1.30691 3.47238 -0.45940 H -1.19950 3.19202 0.14262 H -0.73747 4.76305 0.82866 H 1.84387 2.22584 3.50693 H 3.01542 1.08864 2.89202 H 4.40346 2.14521 0.11562 H 3.07262 -0.24616 0.81319 Traceback (most recent call last): File "/root/anaconda3/bin/dispynode.py", line 208, in _dispy_job_func __dispy_job_name, globals(), localvars) File "<string>", line 1, in <module> File "<string>", line 18, in compute File "./pyscf_geomopt.py", line 99, in hfsto3g mol_sto3g = optimize(mf, grad_cb) File "./pyscf_geomopt.py", line 64, in optimize opt.kernel() File "/root/pyscf/pyscf/geomopt/geometric_solver.py", line 171, in kernel maxsteps=self.max_cycle, **self.params) File "/root/pyscf/pyscf/geomopt/geometric_solver.py", line 119, in kernel constraints=constraints, **kwargs) File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 1708, in run_optimizer progress = Optimize(coords, M, IC, engine, dirname, params, xyzout) File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 1300, in Optimize return optimizer.optimizeGeometry() File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 1265, in optimizeGeometry self.step() File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 1076, in step self.checkCoordinateSystem(recover=True, cartesian=LastForce) File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/optimize.py", line 946, in checkCoordinateSystem if self.IC.repr_diff(IC1) != "": File "/root/anaconda3/lib/python3.7/site-packages/geometric-0.9.4+15.g75989d0-py3.7.egg/geometric/internal.py", line 3021, in repr_diff return self.Prims.repr_diff(other.Prims)AttributeError: 'CartesianCoordinates' object has no attribute 'Prims' — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABvWxK4OAwiwqWlSvoMUV7gk-AZzrjhKks5vWMNngaJpZM4bsv2d> .

[leeping]

Hi there,

@sunqm just pointed me to this issue. There are a few layers to it:

1. I fixed the repr_diff() function so that it should no longer throw an error when comparing DelocalizedInternalCoordinates with PrimitiveInternalCoordinates. It should be fixed in Fix repr_diff() function leeping/geomeTRIC#70 .
2. The line self.checkCoordinateSystem(recover=True, cartesian=LastForce) is not often called, and indicates a critical failure of the geometry optimizer that I haven't encountered recently. However, I'm not able to reproduce the failure locally, as when I set up this job (using HF/3-21G and TeraChem as the QM engine) the geometry optimizer performs normally.
3. The input molecule has a very strange geometry. Are you sure this is what you intended?

Original:

Optimized:

[sunqm]

I believe this must be a corner case. We are also not able to reproduce this error again. Thanks Leeping for solving this issue.