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Fix a bug in run_abacus_md and delete redundant line about gamma_only. #850

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merged 4 commits into from
Aug 7, 2022
Merged

Fix a bug in run_abacus_md and delete redundant line about gamma_only. #850

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ce94cf4
debug: modify gen.py
hongriTianqi Aug 7, 2022
ddcd417
debug: due not to update nstep to md_nstep
hongriTianqi Aug 7, 2022
aff14cb
debug: smearing_method miss gauss
hongriTianqi Aug 7, 2022
e0e8b6e
docs: modify README.md
hongriTianqi Aug 7, 2022
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6 changes: 2 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -147,7 +147,7 @@ If you want to specify a structure as starting point for `init_bulk`, you may se
```
`init_bulk` support both VASP and ABACUS for first-principle calculation. You can choose the software by specifying the key `init_fp_style`. If `init_fp_style` is not specified, the default software will be VASP.

When using ABACUS for `init_fp_style`, the keys of the paths of `INPUT` files for relaxation and MD simulations are the same as `INCAR` for VASP, which are `relax_incar` and `md_incar` respectively. Use `relax_kpt` and `md_kpt` for the relative path for `KPT` files of relaxation and MD simulations. They two can be ommited if `kspacing` or `gamma_only` has been set in corresponding INPUT files. If `from_poscar` is set to `false`, you have to specify `atom_masses` in the same order as `elements`.
When using ABACUS for `init_fp_style`, the keys of the paths of `INPUT` files for relaxation and MD simulations are the same as `INCAR` for VASP, which are `relax_incar` and `md_incar` respectively. Use `relax_kpt` and `md_kpt` for the relative path for `KPT` files of relaxation and MD simulations. They two can be ommited if `kspacing` (in unit of 1/Bohr) or `gamma_only` has been set in corresponding INPUT files. If `from_poscar` is set to `false`, you have to specify `atom_masses` in the same order as `elements`.

The following table gives explicit descriptions on keys in `PARAM`.

Expand All @@ -173,9 +173,7 @@ The bold notation of key (such as **Elements**) means that it's a necessary key.
| type_map | List | [ "Mg", "Al"] | The indices of elements in deepmd formats will be set in this order.
| init_fp_style | String | "ABACUS" or "VASP" | First-principle software. If this key is abscent, the default value will be "VASP".
| relax_kpt | String | "....../KPT" | Path of `KPT` file for relaxation in stage 1. Only useful if `init_fp_style` is "ABACUS".
| relax_kspacing | Integer or List of 3 integers | 10 | kspacing parameter for relaxation in stage 1. Only useful if `init_fp_style` is "ABACUS".
| md_kpt | String | "....../KPT" | Path of `KPT` file for MD simulations in stage 3. Only useful if `init_fp_style` is "ABACUS".
| md_kspacing | Integer or List of 3 integers | 10 | kspacing parameter for MD simulations in stage 3. Only useful if `init_fp_style` is "ABACUS".
| atom_masses | List of float | [24] | List of atomic masses of elements. The order should be the same as `Elements`. Only useful if `init_fp_style` is "ABACUS".

### Init_surf
Expand Down Expand Up @@ -572,7 +570,7 @@ The bold notation of key (such aas **type_map**) means that it's a necessary key
| **user_fp_params** | Dict | |Parameters for ABACUS INPUT. find detail [Here](https://github.com/deepmodeling/abacus-develop/blob/develop/docs/input-main.md#out-descriptor). If `deepks_model` is set, the model file should be in the pseudopotential directory. You can also set `KPT` file by adding `k_points` that corresponds to a list of six integers in this dictionary. Any key beginning with "_" will be ignored.
| **fp_incar** | String | "./abacus/INPUT" | INPUT file for ABACUS. This is another way of providing input parameters. Users must choose one of these two ways. Any keywords beginning with "_" will be ignored
| **k_points** | List of integers | [2,2,2,0,0,0] | Monkhorst-Pack k-grids setting for generating KPT file of ABACUS
| **fp_kpt_file** | String | "./abacus/KPT" | KPT file for ABACUS. This is another way to provide KPT file for ABACUS and has lower priority than the above `k_points` key. They two have lower priority than kspacing and gamma_only in INPUT file of ABACUS.
| **fp_kpt_file** | String | "./abacus/KPT" | KPT file for ABACUS. This is another way to provide KPT file for ABACUS and has lower priority than the above `k_points` key. They two have lower priority than kspacing (in unit of 1/Bohr) and gamma_only in INPUT file of ABACUS.
| **fp_orb_files** | List | |List of atomic orbital files. The files should be in pseudopotential directory.
| **fp_dpks_descriptor** | String | |DeePKS descriptor file name. The file should be in pseudopotential directory.

Expand Down
21 changes: 7 additions & 14 deletions dpgen/data/gen.py
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Expand Up @@ -1159,11 +1159,6 @@ def coll_abacus_md(jdata) :
os.chdir(cwd)

def run_abacus_relax(jdata, mdata):
relax_incar = jdata['relax_incar']
standard_incar = get_abacus_input_parameters(relax_incar) # a dictionary in which all of the values are strings
if "gamma_only" in standard_incar:
if type(standard_incar["gamma_only"])==str:
standard_incar["gamma_only"] = int(eval(standard_incar["gamma_only"]))
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
fp_resources = mdata['fp_resources']
Expand All @@ -1179,6 +1174,8 @@ def run_abacus_relax(jdata, mdata):
dpks_descriptor_name = [os.path.basename(jdata['dpks_descriptor'])]
if 'dpks_model' in jdata:
dpks_model_name = [os.path.basename(jdata['dpks_model'])]
relax_incar = jdata['relax_incar']
standard_incar = get_abacus_input_parameters(relax_incar) # a dictionary in which all of the values are strings
forward_files = ["STRU", "INPUT"]
if "kspacing" not in standard_incar:
forward_files = ["STRU", "INPUT", "KPT"]
Expand Down Expand Up @@ -1298,11 +1295,6 @@ def run_vasp_md(jdata, mdata):
submission.run_submission()

def run_abacus_md(jdata, mdata):
md_incar = jdata['md_incar']
standard_incar = get_abacus_input_parameters(md_incar) # a dictionary in which all of the values are strings
if "gamma_only" in standard_incar:
if type(standard_incar["gamma_only"])==str:
standard_incar["gamma_only"] = int(eval(standard_incar["gamma_only"]))
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
fp_resources = mdata['fp_resources']
Expand All @@ -1321,9 +1313,10 @@ def run_abacus_md(jdata, mdata):
dpks_descriptor_name = [os.path.basename(jdata['dpks_descriptor'])]
if 'dpks_model' in jdata:
dpks_model_name = [os.path.basename(jdata['dpks_model'])]
md_incar = jdata['md_incar']
standard_incar = get_abacus_input_parameters(md_incar) # a dictionary in which all of the values are strings
forward_files = ["STRU", "INPUT"]
if not (("kspacing" in standard_incar) or \
("gamma_only" in standard_incar and standard_incar["gamma_only"]==1)):
if "kspacing" not in standard_incar:
forward_files = ["STRU", "INPUT", "KPT"]
forward_files += orb_file_names + dpks_descriptor_name + dpks_model_name
for pp_file in [os.path.basename(a) for a in jdata['potcars']]:
Expand Down Expand Up @@ -1427,9 +1420,9 @@ def gen_init_bulk(args) :
elif jdata['init_fp_style'] == "ABACUS":
standard_incar = get_abacus_input_parameters(md_incar) # a dictionary in which all of the values are strings
nsw_flag = False
if "nstep" in standard_incar:
if "md_nstep" in standard_incar:
nsw_flag = True
nsw_steps = int(standard_incar['nstep'])
nsw_steps = int(standard_incar['md_nstep'])
if nsw_flag:
if (nsw_steps != md_nstep_jdata):
dlog.info("WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!")
Expand Down
2 changes: 1 addition & 1 deletion dpgen/generator/lib/abacus_scf.py
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Expand Up @@ -75,7 +75,7 @@ def make_abacus_scf_input(fp_params):
assert(fp_params["ks_solver"] in ["cg", "dav", "lapack", "genelpa", "hpseps", "scalapack_gvx"]), "'ks_sover' should in 'cgx', 'dav', 'lapack', 'genelpa', 'hpseps', 'scalapack_gvx'."
ret += "ks_solver %s\n" % fp_params["ks_solver"]
elif key == "smearing_method":
assert(fp_params["smearing_method"] in ["gaussian", "fd", "fixed", "mp", "mp2", "mv"]), "'smearing_method' should in 'gaussian', 'fd', 'fixed', 'mp', 'mp2', 'mv'. "
assert(fp_params["smearing_method"] in ["gauss","gaussian", "fd", "fixed", "mp", "mp2", "mv"]), "'smearing_method' should in 'gauss', 'gaussian', 'fd', 'fixed', 'mp', 'mp2', 'mv'. "
ret += "smearing_method %s\n" % fp_params["smearing_method"]
elif key == "smearing_sigma":
fp_params["smearing_sigma"] = float(fp_params["smearing_sigma"])
Expand Down