gabor1
commented
4 years ago Paste here the first few lines of your XYZ file.
-- Gábor
On 19 Apr 2020, at 07:02, tiandijunhao notifications@github.com wrote:
Hello,
When I put several datasets into a XYZ file for training, the following error is always reported:
fields[0] = Nb, length 2 fields[1] = 0.00000000, length 10 fields[2] = 0.00000000, length 10 fields[3] = 0.00000000, length 10 fields[4] = 0.00000000, length 10 fields[5] = -0.00000000, length 11 fields[6] = -0.00000000, length 11 fields[7] = , length 1 SYSTEM ABORT: Traceback (most recent call last) File "/BIGDATA1/caep_swcc_hygeng_1/software/QUIP-public/src/libAtoms/xyz.c", line 1047 kind IO incomplete row, frame 0 atom 0 - got 8/7 entries line 0
libAtoms::Hello World: 19/04/2020 13:51:41 libAtoms::Hello World: git version NOT_A_GIT_REPOSITORY libAtoms::Hello World: QUIP_ARCH linux_x86_64_gfortran libAtoms::Hello World: compiled on Apr 13 2020 at 14:14:16 libAtoms::Hello World: Random Seed = 49901384 libAtoms::Hello World: global verbosity = 0
Calls to system_timer will do nothing by default
================================ Input parameters ==============================
atoms_filename = //MANDATORY// at_file = Nb_54.xyz gap = "soap l_max=12 n_max=12 cutoff=5.0 cutoff_transition_width=1.0 delta=1.0 atom_sigma=0.5 zeta=4 config_type_n_sparse={elastics:100:md_300k:500:md_1200k:500:default:1000} sparse_method=cur_points covariance_type=dot_product" e0 = Nb:-0.70796320 local_property0 = 0.0 e0_offset = 0.0 e0_method = isolated default_kernel_regularisation = //MANDATORY// default_sigma = "0.005 0.2 1.0 0.0" sparse_jitter = 1e-12 hessian_displacement = 1.0e-2 hessian_delta = 1.0e-2 baseline_param_filename = quip_params.xml core_param_file = quip_params.xml baseline_ip_args = core_ip_args = energy_parameter_name = free_energy local_property_parameter_name = local_property force_parameter_name = forces virial_parameter_name = stress hessian_parameter_name = hessian config_type_parameter_name = config_type kernel_regularisation_parameter_name = sigma sigma_parameter_name = sigma config_type_kernel_regularisation = config_type_sigma = elastics:0.0001:0.01:0.01:0.0:md_300k:0.001:0.05:1.0:0.0:md_1200k:0.001:0.05:1.0:0.0 kernel_regularisation_is_per_atom = T sigma_per_atom = T do_copy_atoms_file = T do_copy_at_file = F sparse_separate_file = T sparse_use_actual_gpcov = F gap_file = gap_new.xml gp_file = GAP_Nb.xml verbosity = NORMAL rnd_seed = -1 do_ip_timing = F template_file = template.xyz sparsify_only_no_fit = F
======================================== ======================================
============== Gaussian Approximation Potentials - Database fitting ============
Initial parsing of command line arguments finished. Found 1 GAPs. Descriptors have been parsed When I train different data sets separately, it can be carried out normally.
This is my command：
gap_fit energy_parameter_name=free_energy force_parameter_name=forces virial_parameter_name = stress do_copy_at_file=F sparse_separate_file=T gp_file=GAP_Nb.xml at_file=Nb_54.xyz \ gap={soap l_max=12 n_max=12 \ cutoff=5.0 cutoff_transition_width=1.0 delta=1.0 \ atom_sigma=0.5 zeta=4 config_type_n_sparse={elastics:100:md_300k:500:md_1200k:500:default:2000} \ sparse_method=cur_points \ covariance_type=dot_product} \ sparse_jitter=1e-12 \ default_sigma={0.005 0.2 1.0 0.0} \ config_type_sigma={elastics:0.0001:0.01:0.01:0.0:md_300k:0.001:0.05:1.0:0.0:md_1200k:0.001:0.05:1.0:0.0} \ e0={Nb:-0.70796320} How can I solve it?
Best regards， Wang
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tiandijunhao
Hello,
When I put several datasets into a XYZ file for training, the following error is always reported:
When I train different data sets separately, it can be carried out normally.
This is my command：
How can I solve it?
Best regards， Wang