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View Code? Open in Web Editor NEWANI-1 neural net potential with python interface (ASE)
License: MIT License
ANI-1 neural net potential with python interface (ASE)
License: MIT License
Hi,
I wonder if there are some guidelines to build ASE_INI with CUDA/11.7.0 and python 3.9.6? CUDA 9 is not longer supported in our HPC center. Thanks.
Hello!
Thanks very much for this open-source project. It has been a great experience.
I would like to ask you fever.
Recently, I have bought a new PC with one component, Nvidia Geforce RTX 3080.
When I was running ani_quicktest.py after I installed ASE_ANI and related essential software, I got an error:
python ani_quicktest.py
ERROR: CUDA throw detected! Attempting to shut down nicely!
CUDA Error -- "invalid device symbol"
13 in location -- /home/jujuman/Gits/NeuroChem/src-aevlib/cuda_aev/cuaev_compute.cu:1939
in function -- cuaev_compute_base()Traceback (most recent call last):
File "ani_quicktest.py", line 21, in
mol.set_calculator(ANIENS(aniensloader('../ani_models/ani-1ccx_8x.info',0)))
File "/home/micro/local/ASE_ANI/lib/ase_interface.py", line 1038, in aniensloader
return ensemblemolecule(cnstfile, saefile, nnfdir, Nn, gpu)
File "/home/micro/local/ASE_ANI/lib/ase_interface.py", line 477, in init
self.ncl = [pync.molecule(cnstfile, saefile, nnfprefix + str(i+net_start_id) + '/networks/', 1, gpuid, sinet) for i in
File "/home/micro/local/ASE_ANI/lib/ase_interface.py", line 477, in
self.ncl = [pync.molecule(cnstfile, saefile, nnfprefix + str(i+net_start_id) + '/networks/', 1, gpuid, sinet) for i in
RuntimeError: unidentifiable C++ exception
I assumed that it may be due to Nvidia Geforce RTX 3080 having a new device symbol,
however, I could not solve the problem by myself.
Would you have some ideas to solve it?
Any help would be much appreciated.
Let me inform you of an overview of the PC:
Operating system: Ubuntu Desktop 18.04.5
Nvidia driver version: Driver Version: 460.32.03
CUDA toolkit version: 9.2
Python version: 3.8.5
CPU: Intel(R) Core(TM) i9-10900F CPU @ 2.80GHz
Memory: 64 GB
GPU: Nvidia Geforce RTX 3080 (10GB)
Best regards,
Teruo.
Please do not use it at the moment
without training slash:
ERROR: ANNP throw detected! Attempting to shut down nicely!
FPN Error -- "Network not found for ANNP_LOAD_HDNN_AND_TEST!"
in location -- /home/jujuman/Gits/NeuroChem/src-atomicnnplib/cunetwork/neuralnetbase.cu:98
in function -- cuNeuralNetworkbase()
Another point that wasn't mentioned in the paper is if you guys were training to the total QM energy or the Atomization Energies (since you guys do provide the self-interaction atomic energies). Can you kindly clarify?
Hello, I'm just getting started with ASE_ANI and am trying to make sure the simple ani_quicktest.py
runs before I try anything else. I noticed what seem to be some python type problems that I'm hoping you could help with.
Once I got everything installed correctly and was able to run it (python ani_quicktest.py
in the example folder) this is the output I got:
van Der Waals correction will be unavailable. Please install ased3
Traceback (most recent call last):
File "ani_quicktest.py", line 24, in <module>
ei = mol.get_potential_energy()
File "/home/cbannan/.local/lib/python3.6/site-packages/ase/atoms.py", line 674, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/home/cbannan/.local/lib/python3.6/site-packages/ase/calculators/calculator.py", line 618, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/home/cbannan/.local/lib/python3.6/site-packages/ase/calculators/calculator.py", line 668, in get_property
self.calculate(atoms, [name], system_changes)
File "/home/cbannan/ANI/ASE_ANI/lib/ase_interface.py", line 689, in calculate
self.nc.set_cell((self.atoms.get_cell()).astype(np.float32), pbc_inv)
AttributeError: 'Cell' object has no attribute 'astype'
After some digging into ase.Atoms
and ase.cell.Cell
, it became clear that the Cell object does not in fact have a method astype
. Looking at other lines of code in ase_interface
I noticed that on line 687 this call np.linalg.inv(self.atoms.get_cell())).astype(np.float32)
works just fine which made me assume the astype needed an np.arrary
instead of an ase.cell.Cell
. I decided to try changing the Cell
object to an array
in line 689 with this change:
self.nc.set_cell(np.arrary(self.atoms.get_cell()).astype(np.float32), pbc_inv)
This appeared to "fix" things in that at least when I reran the script I got different out:
van Der Waals correction will be unavailable. Please install ased3
With Caitlin's change
Initial Energy: -2078.5028228165684
Optimizing...
Traceback (most recent call last):
File "ani_quicktest.py", line 31, in <module>
dyn.run(fmax=0.001)
File "/home/cbannan/.local/lib/python3.6/site-packages/ase/optimize/optimize.py", line 246, in run
return Dynamics.run(self)
File "/home/cbannan/.local/lib/python3.6/site-packages/ase/optimize/optimize.py", line 159, in run
for converged in Dynamics.irun(self):
File "/home/cbannan/.local/lib/python3.6/site-packages/ase/optimize/optimize.py", line 125, in irun
self.atoms.get_forces()
File "/home/cbannan/.local/lib/python3.6/site-packages/ase/atoms.py", line 728, in get_forces
forces = self._calc.get_forces(self)
File "/home/cbannan/.local/lib/python3.6/site-packages/ase/calculators/calculator.py", line 632, in get_forces
return self.get_property('forces', atoms)
File "/home/cbannan/.local/lib/python3.6/site-packages/ase/calculators/calculator.py", line 668, in get_property
self.calculate(atoms, [name], system_changes)
File "/home/cbannan/ANI/ASE_ANI/lib/ase_interface.py", line 703, in calculate
self.nc.set_cell((self.atoms.get_cell()).astype(np.float32), pbc_inv)
AttributeError: 'Cell' object has no attribute 'astype'
So now line 703 seems to have the same problem 689 did. So I changed line 703 to:
self.nc.set_cell(np.array(self.atoms.get_cell()).astype(np.float32), pbc_inv)
Finally I was able to run the ani_quicktest.py
without any errors and got the energies as:
Initially, I didn't install ased3 because I was under the impression it was optional and I wanted to make sure that I could run the script as is. However, now I've noticed that ased3 also doesn't have a license associated with it which makes me hesitant to try it. Do you know if this same issue will come up if I include ased3?
Thanks for your help in advance!
Hello,
I am trying to setting up ASE-ANI in my box with Linux Mint 19.1
When I run the test, I got:
python3 ~/bin/ASE_ANI/examples/ani_quicktest.py van Der Waals correction will be unavailable. Please install ased3 Traceback (most recent call last): File "/home/icamps/bin/ASE_ANI/examples/ani_quicktest.py", line 16, in <module> mol = read('data/water.xyz') File "/usr/lib/python3/dist-packages/ase/io/formats.py", line 428, in read parallel=parallel, **kwargs)) File "/usr/lib/python3/dist-packages/ase/io/formats.py", line 475, in _iread fd = open_with_compression(filename) File "/usr/lib/python3/dist-packages/ase/io/formats.py", line 286, in open_with_compression return open(filename, mode) FileNotFoundError: [Errno 2] No such file or directory: 'data/water.xyz'
But trying to install ASED3, I got then (with python setup.py install):
gfortran: error: build/temp.linux-x86_64-2.7/ased3/_d3params.o: No such file or directory gfortran: error: build/temp.linux-x86_64-2.7/ased3/_d3.o: No such file or directory gfortran: error: build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ased3/_d3-f2pywrappers2.o: No such file or directory
If I execute python3 setup.py install
I got:
build/src.linux-x86_64-3.6/ased3/_d3module.c:17:10: fatal error: Python.h: No such file or directory #include "Python.h" ^~~~~~~~~~ compilation terminated. build/src.linux-x86_64-3.6/ased3/_d3module.c:17:10: fatal error: Python.h: No such file or directory #include "Python.h" ^~~~~~~~~~ compilation terminated. error: Command "x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ased3 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c build/src.linux-x86_64-3.6/ased3/_d3module.c -o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ased3/_d3module.o -MMD -MF build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ased3/_d3module.o.d" failed with exit status 1
I appreciate any help.
Regards,
Camps
Hi guys,
I want to confirm that you guys are still using the exponential loss function. i.e. you're taking the exponential of the sum of squared errors, and not, the sum of the exponential of the squared errors. I'm running into overflow problems where exp^(sum of squared errors) is so that big that it's causing overflow problems.
Hello, I am trying the ani_quicktest.py
example and I receive an error:
$ python examples/ani_quicktest.py
Traceback (most recent call last):
File "/home/mdi0316/WORK_TME022/external_packages/ASE_ANI/examples/ani_quicktest.py", line 6, in <module>
from ase_interface import ANIENS
File "/home/mdi0316/WORK_TME022/external_packages/ASE_ANI/lib/ase_interface.py", line 20, in <module>
import pyNeuroChem as pync
ImportError: libcublas.so.9.2: cannot open shared object file: No such file or directory
Nonetheless, I installed libcublas
$ conda list | grep libcublas
libcublas 12.3.2.9 0 nvidia
I am using this GPU:
$ sudo lshw -C display
[sudo] password for mdi0316:
*-display
description: VGA compatible controller
product: GM204GL [Quadro M4000]
vendor: NVIDIA Corporation
physical id: 0
bus info: pci@0000:02:00.0
version: a1
width: 64 bits
clock: 33MHz
capabilities: pm msi pciexpress vga_controller bus_master cap_list rom
configuration: driver=nvidia latency=0
resources: irq:40 memory:f2000000-f2ffffff memory:e0000000-efffffff memory:f0000000-f1ffffff ioport:1000(size=128) memory:c0000-dffff
Thank you
Dear developers,
I'm running "ensemble_molecular_dynamics.ipynb" in example folder with a different geometry. I got the following error during the geometry optimization. It seems like some location is hard-coded to the developer's environment. How you have any suggestions to fix it?
ERROR: CUDA throw detected! Attempting to shut down nicely!
CUDA Error -- "an illegal memory access was encountered"
77 in location -- /nh/nest/u/jsmith/scratch/Gits/NeuroChem/src-aevlib/cuda_aev/cuaev_compute.cu:2511
in function -- v_compute_aevec_components()
Traceback (most recent call last):
File "ensemble_molecular_dynamics.py", line 73, in
dyn.run(fmax=0.001)
File "/home/.local/lib/python3.6/site-packages/ase/optimize/optimize.py", line 202, in run
for converged in self.irun(fmax, steps):
File "/home/.local/lib/python3.6/site-packages/ase/optimize/optimize.py", line 175, in irun
self.set_force_consistent()
File "/home/.local/lib/python3.6/site-packages/ase/optimize/optimize.py", line 245, in set_force_consistent
self.atoms.get_potential_energy(force_consistent=True)
File "/home/.local/lib/python3.6/site-packages/ase/atoms.py", line 662, in get_potential_energy
self, force_consistent=force_consistent)
File "/home/.local/lib/python3.6/site-packages/ase/calculators/calculator.py", line 505, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/home/.local/lib/python3.6/site-packages/ase/calculators/calculator.py", line 552, in get_property
self.calculate(atoms, [name], system_changes)
File "/home/software/ASE_ANI/lib/ase_interface.py", line 706, in calculate
energy, force, stddev, Fstddev = self.nc.compute_mean_props()
File "/home/software/ASE_ANI/lib/ase_interface.py", line 481, in compute_mean_props
self.E[i] = nc.energy().copy()
RuntimeError: unidentifiable C++ exception
Trying to debug some PBC issues I'm seeing with various implementations of ANI under PBC. Using an in house implementation or Torchani the energy drifts. I wanted to test with this code base but computing the energy of a benzene crystal resulted in a RuntimeError:
Traceback (most recent call last): [0/1949]
File "../ani_utilities/optimize_crystal.py", line 168, in
main()
File "../ani_utilities/optimize_crystal.py", line 153, in main
energy = single_point_energy(atoms, calculator)
File "/home/jacobson/ani_utilities/utils.py", line 27, in single_point_energy
energy = molecule.get_potential_energy()/EV
File "/home/jacobson/ase_ani_venv36/lib/python3.6/site-packages/ase/atoms.py", line 664, in get_potential_e
nergy
energy = self._calc.get_potential_energy(self)
File "/home/jacobson/ase_ani_venv36/lib/python3.6/site-packages/ase/calculators/calculator.py", line 505, i
n get_potential_energy
energy = self.get_property('energy', atoms)
File "/home/jacobson/ase_ani_venv36/lib/python3.6/site-packages/ase/calculators/calculator.py", line 552, i
n get_property
self.calculate(atoms, [name], system_changes)
File "/home/jacobson/ASE_ANI/lib/ase_interface.py", line 710, in calculate
energy, force, stddev, Fstddev = self.nc.compute_mean_props()
File "/home/jacobson/ASE_ANI/lib/ase_interface.py", line 482, in compute_mean_props
self.F[i] = nc.force().copy()
RuntimeError: unidentifiable C++ exception
ERROR: CUDA throw detected! Attempting to shut down nicely!
CUDA Error -- "an illegal memory access was encountered"
77 in location -- /nh/nest/u/jsmith/scratch/Gits/NeuroChem/src-atomicnnplib/cunetwork/cuannlayer_t.cu:634
in function -- m_clearDataOnDevice()
terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits, std:
:allocator >'
Aborted (core dumped)
The geometry I'm using is from the CCD, here is some data if you want to locate it:
data_BENZEN11 [38/1866]
_audit_creation_date 2006-03-08
_database_code_depnum_ccdc_archive 'CCDC 298305'
_journal_coeditor_code 'IUCr AV5045'
_chemical_formula_moiety 'C6 H6'
_chemical_name_systematic Benzene
_journal_coden_Cambridge 622
_journal_volume 62
_journal_year 2006
_journal_page_first 94
_journal_name_full 'Acta Crystallogr.,Sect.B:Struct.Sci.'
Regards
It would be nice to have a way to automatically install all requirements and dependencies.
Hi there,
Thank you for sharing this code! I'm trying to install the OpenMM plugin from chemalot (https://github.com/chemalot/openmm-ani), and it seems that some libraries are required from ASE_ANI. I think the missing library is neurochemcpp_iface.h, which is in your repository for CentOS versions. Do you also have a version for ubuntu with cuda 9.2 and python 3.6? Thanks a ton! -Virginia
ps The ASE_ANI code works very well for me, so this isn't actually an ASE_ANI issue.
Thanks fro making this available this is very exciting research!
Ever since reading the papers I have been asking myself if it is really necessary to sample the angular shift from -PI to +PI?
It seems to me that you can not distinguish positive from negative angles and therefore should be able to just sample from 0 to PI. Since you are looking at triples of atoms I see no way to define right hand versus left hand angles.
Could you comment on this?
Thanks,
Alberto
Firstly, thank you for sharing this inspiring piece of software.
My question is related to the use of periodicity. Provided the system size is sufficiently large (at least 2 times the maximum cutoff used in the ANI-NPP), the angular-radial symmetry functions should permit a straightforward implementation of periodic boundary conditions within the minimum image convention framework (i.e. always choose the closest image to a given atomic center).
Indeed, i have noticed that there is a setting called pbc set to zero in the associated inputtrain-files.
i) Is it as simple as setting this flag to 1 to invoke a periodic version of the ANI-NPP?!
ii) If yes, is this modification only necessary in the inputtrain file of the master-directory (e.g. ani-1x_8x) or also in each of the inputtrain-files in the respective train-subfolders?
iii) Since ANI is implemented in the framework of ASE, I assume that the cell-definition of ASE are accessed in the ASE ANI interface. Are these unit cells build within the convention of ranging from 0 to L, or from -L/2 to +L/2 (with L being a respective cell dimension)?
Best regards and many thanks,
Thomas Hofer
Ok, how do I install ased3 then?
Hello,
I'm trying to setup ASE_ANI but I have a problem with loading libAtomicNNP library.
I used ctypes library like this:
from ctypes import *
libAtomicNNP= cdll.LoadLibrary('/content/ASE_ANI/lib/libAtomicNNP.so')
but I get this error:
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
<ipython-input-47-b5ad2034551e> in <module>()
----> 1 libAtomicNNP= cdll.LoadLibrary('/content/ASE_ANI/lib/libAtomicNNP.so')
1 frames
/usr/lib/python3.6/ctypes/__init__.py in __init__(self, name, mode, handle, use_errno, use_last_error)
346
347 if handle is None:
--> 348 self._handle = _dlopen(self._name, mode)
349 else:
350 self._handle = handle
OSError: /content/ASE_ANI/lib/libAtomicNNP.so: undefined symbol: _ZN6aevlib18cuaev_compute_file16get_next_datasetERSt6vectorIPfSaIS2_EES5_RS1_ItSaItEE
It seems there are some issues with "c" wrapper in libAtomicNNP.so
I think recreating the .so files, mentionnig boost_threads and systems will solve the problem.
Thanks :)
Saeid
Dear ANI Team,
is it possbile to run a simulation with the ANI FF and include an additional (classical) point charge in the simulation? If yes, how would I do it?
Many thanks and best
Thorren
We're waiting on the full dataset (with augmentation via normal mode sampling) to allow us to do complete validation of the ANI model - @lilleswing recommended using gitLFS for distribution.
Thoughts?
Just curious why you're distributing binary libraries instead of a platform-portable version here. Is the actual code that could be targeted to multiple systems available in another repo?
# ./test.sh
Traceback (most recent call last):
File "~/src/ASE_ANI/examples/ani_quicktest.py", line 6, in <module>
from ase_interface import ANIENS
File "~/src/ASE_ANI/lib/ase_interface.py", line 20, in <module>
import pyNeuroChem as pync
ImportError: ~/src/ASE_ANI/lib/libboost_python.so.1.63.0: undefined symbol: _Py_fopen
Hi guys,
We've heard from the authors of TensorMol (who also were inspired by the fantastic work done by you guys), that training to the force in addition to the total energy can improve accuracy. Do you guys by chance still have the force vectors from gaussian that could be included to the dataset?
What mean and variance are you setting for your Gaussian Activation Functions?
How are you guys doing the splits on the train/valid/test? Are you splitting on chemotypes (i.e. different molecules are lumped together) or splitting on conformations (all conformers are scattered randomly)? I.e. train/test/valid may have mixed chemotypes?
I followed the steps as recommended by the readme file and example bashrc for configuring the models. I am facing the following error while trying to import ANIENS. I attach the command and the trace below. Could you please help me resolve this? I have checked if the LD_LIBRARY_PATH contains the required path and it does.
Command:
from ase_interface import ANIENS
Trace:
van Der Waals correction will be unavailable. Please install ased3
ImportError Traceback (most recent call last)
in
----> 1 from ase_interface import ANIENS
/scratch/e/esargent/mxyptlkr/ml_potential/ASE_ANI/lib/ase_interface.py in
18 pass
19
---> 20 import pyNeuroChem as pync
21
22 import multiprocessing
ImportError: /scratch/e/esargent/mxyptlkr/ml_potential/ASE_ANI/lib/pyNeuroChem.so: cannot open shared object file: No such file or directory
$ python3 examples/ani_quicktest.py
Traceback (most recent call last):
File "~/src/ASE_ANI/examples/ani_quicktest.py", line 6, in <module>
from ase_interface import ANIENS
ModuleNotFoundError: No module named 'ase_interface'
I am trying to use the features implemented in this model. It seems that it should e possible to generate the features given an xyz file. Could you point me to the part of code related to this or show me an example? Thanks!
Hi,
Will ASE_ANI work with cuda newer than 9.0? If not, would it be possible to have it updated to support current CUDA release(s)?
Thanks,
Alex
Can you provide ANI-2X
The paper describes an example of H2O, where the total energy is sum of individual contributions obtained from the two hydrogens and an oxygen. Could you clarify a bit on how the loss is propagated backwards when the model used for the two hydrogens is the same, as only the total energy is available and the individual contributions are unknown while training the model ?
Hi,
When I was trying to understand your code I got confused about the default_neighborlist
method. I thought it should select the atoms within the cutoff range but the result is not the case:
In this example I set cutoff to 1.1 but species with distance > 1.1 are also included. Could you please explain the method's function or is it implemented incorrectly?
Thanks!
I noticed that the parameters in
https://github.com/isayev/ASE_ANI/blob/master/ANI-c08f-ntwk/rHCNO-4.6A_16-3.1A_a4-8.params
differ from what's in the paper
TM = 1
Rcr = 4.6000e+00
Rca = 3.1000e+00
EtaR = [1.6000000e+01]
ShfR = [5.0000000e-01,7.5625000e-01,1.0125000e+00,1.2687500e+00,1.5250000e+00,1.7812500e+00,2.0375000e+00,2.2937500e+00,2.5500000e+00,2.8062500e+00,3.0625000e+00,3.3187500e+00,3.5750000e+00,3.8312500e+00,4.0875000e+00,4.3437500e+00]
Zeta = [8.0000000e+00]
ShfZ = [0.0000000e+00,7.8539816e-01,1.5707963e+00,2.3561945e+00,3.1415927e+00,3.9269908e+00,4.7123890e+00,5.4977871e+00]
EtaA = [6.0000000e+00]
ShfA = [5.0000000e-01,1.1500000e+00,1.8000000e+00,2.4500000e+00]
Atyp = [H,C,N,O]
Namely, this produces a feature vector with 384 as opposed to the ~700 floats mentioned in the paper. In addition, the NN it self seems to be 256x128x64x1 as opposed to 128x128x64x1
!InputFile for Force Prediction Network
sflparamsfile=rHCNO-4.6A_16-3.1A_a4-8.params
ntwkStoreDir=networks/
atomEnergyFile=../../sae_6-31gd.dat
nmax=0! Maximum number of iterations (0 = inf)
tolr=100! Tolerance - early stopping
emult=0.25!Multiplier by eta after tol switch
eta=0.0001! Eta -- Learning rate
tcrit=1.0E-5! Eta termination criterion
tmax=0! Maximum time (0 = inf)
tbtchsz=1024
vbtchsz=1024
gpuid=2
seed=82131921
runtype=ANNP_CREATE_HDNN_AND_TRAIN!Create and train a HDN network
network_setup {
inputsize=384;
layer [
nodes=256;
activation=5;
type=0;
dropout=0;
dropset=0.5;
maskupdate=0.999;
maxnorm=1;
norm=3.0;
normupdate=0.9999;
]
layer [
nodes=128;
activation=5;
type=0;
dropout=0;
dropset=0.5;
maskupdate=0.999;
maxnorm=1;
norm=3.0;
normupdate=0.9999;
]
layer [
nodes=64;
activation=5;
type=0;
dropout=0;
dropset=0.5;
maskupdate=0.999;
maxnorm=1;
norm=3.0;
normupdate=0.9999;
]
layer [
nodes=1;
activation=6;
type=0;
]
}
adptlrn=OFF ! Adaptive learning (OFF,RMSPROP)
decrate=0.9 !Decay rate of RMSPROP
moment=ADAM! Turn on momentum or nesterov momentum (OFF,CNSTTEMP,TMANNEAL,REGULAR,NESTEROV)
mu=0.99 ! Mu factor for momentum
Do you mind clarifying what are the canonical parameters are needed to reproduce the paper given the dataset?
Hi,
How does one know what was the exact data set used to train ANI-2x?
In the original ANI-2x paper, it is said that the training data set is composed of molecules from a variety of sources, including the GDB-11 database, the CheMBL database, the s66x8 benchmark, and some randomly generated amino acids and dipeptides.
Nevertheless, from what I understood, these data sets are not included integrally because some specific sampling techniques are then employed.
Is it possible to know which were the exact molecules used for training?
Thank you.
Best,
João
--- lib/ase_interface.py 2017-07-13 14:29:18.239944902 -0500
+++ lib/ase_interface_.py 2017-07-13 15:04:52.837327087 -0500
@@ -31,18 +31,18 @@
nolabel = True
def __init__(self, build=True,gpuid=0,reslist=[],**kwargs):
- Calculator.__init__(self, **kwargs)
-
if build:
anipath = os.path.dirname(__file__)
- cnstfile = anipath + '/../ANI-c08f-ntwk/rHCNO-4.6A_16-3.1A_a4-8.params'
- saefile = anipath + '/../ANI-c08f-ntwk/sae_6-31gd.dat'
- nnfdir = anipath + '/../ANI-c08f-ntwk/networks/'
+ cnstfile = kwargs.pop('cnstfile', anipath + '/../ANI-c08f-ntwk/rHCNO-4.6A_16-3.1A_a4-8.params')
+ saefile = kwargs.pop('saefile', anipath + '/../ANI-c08f-ntwk/sae_6-31gd.dat')
+ nnfdir = kwargs.pop('nnfdir', anipath + '/../ANI-c08f-ntwk/networks/')
self.nc = pync.molecule(cnstfile, saefile, nnfdir, gpuid)
self.Setup=True
self.reslist=reslist
+ Calculator.__init__(self, **kwargs)
+
def setnc(self,nc):
self.nc = nc
@@ -278,19 +278,20 @@
nolabel = True
def __init__(self, build=True, **kwargs):
- Calculator.__init__(self, **kwargs)
if build:
anipath = os.path.dirname(__file__)
- cnstfile = anipath + '/../ANI-c08e-ntwk/rHCNO-4.6A_16-3.1A_a4-8.params'
- saefile = anipath + '/../ANI-c08e-ntwk/sae_6-31gd.dat'
- nnfdir = anipath + '/../ANI-c08e-ntwk/networks/'
- self.nc = pync.molecule(cnstfile, saefile, nnfdir, 0)
+ cnstfile = kwargs.pop('cnstfile', anipath + '/../ANI-c08f-ntwk/rHCNO-4.6A_16-3.1A_a4-8.params')
+ saefile = kwargs.pop('saefile', anipath + '/../ANI-c08f-ntwk/sae_6-31gd.dat')
+ nnfdir = kwargs.pop('nnfdir', anipath + '/../ANI-c08f-ntwk/networks/')
+ self.nc = pync.molecule(cnstfile, saefile, nnfdir, gpuid)
self.Setup = True
def setnc(self, nc):
self.nc = nc
+ Calculator.__init__(self, **kwargs)
+
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
What is the floating precision used to produce the wB97 DFT energies for the ANI-1 dataset?
Hi, can you please help on the following error?
File "ani_quicktest.py", line 6, in
from ase_interface import ANIENS
File "/ASE_ANI/examples/ase_interface.py", line 20, in
import pyNeuroChem as pync
ImportError: libAEV.so: cannot open shared object file: No such file or directory
What is the state of the experimental support for fluorine and sulfur atoms?
I got the following error when i tried to calculate the potential energy using mol.get_potential_energy()
as described in your example files.
ERROR: AEVLib Fatal Error detected!
FPN Error -- "Cannot find atomic symbol S in internal index. Check your sae file.
"
in location -- /home/jujuman/Gits/NeuroChem/src-aevlib/utilities/datacommander.cpp:57
in function -- get_idx_for_types()
Error detected, terminating!
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