Add support for the new fp_style "cpx" (Quantum Espresso Car-Parrinello cp.x)

doc/overview/supported-software.md

@@ -104,6 +104,14 @@ Configure the INPUT file properly with appropriate basis sets and k-point sampli
 
 Ensure proper pseudopotential selection and k-point convergence for calculations. The extensive documentation and large user community provide good support for troubleshooting.
 
+### CPMD (Quantum ESPRESSO)
+
+{dargs:argument}`fp_style <run_jdata/fp_style>`: `cpx`
+
+CPMD (Car-Parrinello Molecular Dynamics) is another integration from [Quantum ESPRESSO](https://www.quantum-espresso.org/) suite, specifically the `cp.x` executable. This interface is well-suited for calculating energies and forces of various types of structures, even large molecules, using Car-Parrinello method. It utilizes a plane-wave basis set and pseudopotentials, optimized for efficient molecular dynamics simulations.
+
+To use it with DP-GEN, one must prepare a template for the `cp.x` program configured for an electron relaxation procedure to obtain accurate ground-state properties, which is usually achieved after several tens to several hundred minimization steps. Be cautious to set `iprint` equal to `nstep` to ensure the output contains the final relaxed structure and its properties. Other key configuration requirements for the template are: both `ATOMIC_POSITIONS` and `CELL_PARAMETERS` cards must contain the `{angstrom}` keyword; the `%POSITIONS%` string must be in place of actual atomic coordinates, while the `%CELL%` string must be in place of actual cell vectors. It is also recommended to use absolute path for pseudopotentials. Ensure proper pseudopotential selection and electron dynamics configuration for reliable results.
+
 ### PWmat
 
 {dargs:argument}`fp_style <run_jdata/fp_style>`: `pwmat`

dpgen/generator/arginfo.py

@@ -933,6 +933,31 @@ def fp_style_pwscf_args() -> list[Argument]:
     ]
 
 
+def fp_style_cpx_args() -> list[Argument]:
+    """Arguments for FP style cpx (Car-Parrinello Quantum Espresso).
+
+    Returns
+    -------
+    list[dargs.Argument]
+        list of cpx fp style arguments
+    """
+    doc_fp_params_cpx = "Parameters for FP calculation."
+    doc_input_fn = "Input file name for cp.x without file extension (.in). Essentially must be the same as the prefix in the template."
+    doc_template = "Template file name. Is used for completing the input file. Should contain all necessary FP configurations besides ATOMIC_POSITIONS and CELL_PARAMETERS"
+    return [
+        Argument(
+            "fp_params",
+            dict,
+            optional=False,
+            doc=doc_fp_params_cpx,
+            sub_fields=[
+                Argument("input_fn", str, optional=False, doc=doc_input_fn),
+                Argument("template_fn", str, optional=False, doc=doc_template),
+            ],
+        ),
+    ]
+
+
 def fp_style_custom_args() -> list[Argument]:
     """Arguments for FP style custom.
 
@@ -990,6 +1015,7 @@ def fp_style_variant_type_args() -> Variant:
             ),
             Argument("pwmat", dict, [], doc="TODO: add doc"),
             Argument("pwscf", dict, fp_style_pwscf_args()),
+            Argument("cpx", dict, fp_style_cpx_args()),
             Argument("custom", dict, fp_style_custom_args(), doc=doc_custom),
         ],
         optional=False,

dpgen/generator/run.py

@@ -3902,6 +3902,53 @@ def make_fp_amber_diff(iter_index: int, jdata: dict):
     os.chdir(cwd)
 
 
+def make_fp_cpx(iter_index, jdata):
+    """Make input file for Quantum Espresso Car-Parrinello (cp.x) run.
+
+    Convert the POSCAR file to cp.x input file using prepared template.
+
+    Parameters
+    ----------
+    iter_index : int
+        iter index
+    jdata : dict
+        Run parameters.
+    """
+    work_path = os.path.join(make_iter_name(iter_index), fp_name)
+    fp_tasks = glob.glob(os.path.join(work_path, "task.*"))
+    fp_params = jdata["fp_params"]
+    input_fn = fp_params["input_fn"]
+    template_fn = fp_params["template_fn"]
+
+    with open(template_fn) as tn:
+        template = tn.read()
+
+    for ii in fp_tasks:
+        itemp = copy.deepcopy(template)
+        with set_directory(Path(ii)):
+            system = dpdata.System("POSCAR", fmt="vasp/poscar")
+            # convert POSCAR to cp.in
+            cell_param = ""
+            for a in system["cells"][0]:
+                for v in a:
+                    cell_param += f"{v:.16e} "
+                cell_param += "\n"
+            itemp = itemp.replace("%CELL%", cell_param)
+
+            pos = ""
+            ntypes = system.get_ntypes()
+            numbs = system.get_atom_numbs()
+            names = system.get_atom_names()
+            coords = system["coords"][0]
+            for t in range(ntypes):
+                ts = sum(numbs[:t])
+                for a in range(numbs[t]):
+                    pos += f"{names[t]:2} {coords[a + ts, 0]:20.16f} {coords[a + ts, 1]:20.16f} {coords[a + ts, 2]:20.16f}\n"
+            itemp = itemp.replace("%POSITIONS%", pos)
+            with open(input_fn + ".in", "w") as fp:
+                fp.write(itemp)
+
+
 def make_fp_custom(iter_index, jdata):
     """Make input file for customized FP style.
 
@@ -3973,6 +4020,8 @@ def make_fp_calculation(iter_index, jdata, mdata):
         make_fp_pwmat(iter_index, jdata)
     elif fp_style == "amber/diff":
         make_fp_amber_diff(iter_index, jdata)
+    elif fp_style == "cpx":
+        make_fp_cpx(iter_index, jdata)
     elif fp_style == "custom":
         make_fp_custom(iter_index, jdata)
     else:
@@ -4280,6 +4329,20 @@ def run_fp(iter_index, jdata, mdata):
             log_file="output",
             forward_common_files=forward_common_files,
         )
+    elif fp_style == "cpx":
+        extensions = [".cel", ".evp", ".for", ".pos", ".str"]
+        input_fn = jdata["fp_params"]["input_fn"]
+        forward_files = [input_fn + ".in"]
+        backward_files = [input_fn + ext for ext in extensions] + ["output"]
+        run_fp_inner(
+            iter_index,
+            jdata,
+            mdata,
+            forward_files,
+            backward_files,
+            _qe_check_fin,
+            log_file="output",
+        )
     elif fp_style == "custom":
         fp_params = jdata["fp_params"]
         forward_files = [fp_params["input_fn"]]
@@ -4750,6 +4813,50 @@ def post_fp_amber_diff(iter_index, jdata):
         all_sys.to_deepmd_npy(sys_data_path, set_size=len(sys_output), prec=np.float64)
 
 
+def post_fp_cpx(iter_index, jdata):
+    """Post fp for cp.x. Collect data from qe/cp/traj labeled system.
+
+    Parameters
+    ----------
+    iter_index : int
+        The index of the current iteration.
+    jdata : dict
+        The parameter data.
+    """
+    model_devi_jobs = jdata["model_devi_jobs"]
+    assert iter_index < len(model_devi_jobs)
+
+    iter_name = make_iter_name(iter_index)
+    work_path = os.path.join(iter_name, fp_name)
+    fp_tasks = glob.glob(os.path.join(work_path, "task.*"))
+    fp_tasks.sort()
+    if len(fp_tasks) == 0:
+        return
+
+    system_index = []
+    for ii in fp_tasks:
+        system_index.append(os.path.basename(ii).split(".")[1])
+    system_index.sort()
+    set_tmp = set(system_index)
+    system_index = list(set_tmp)
+    system_index.sort()
+
+    fp_params = jdata["fp_params"]
+    input_fn = fp_params["input_fn"]
+
+    for ss in system_index:
+        sys_output = glob.glob(os.path.join(work_path, f"task.{ss}.*"))
+        sys_output.sort()
+        all_sys = dpdata.MultiSystems(type_map=jdata["type_map"])
+        for oo in sys_output:
+            if os.path.exists(os.path.join(oo, "output")):
+                sys = dpdata.LabeledSystem(os.path.join(oo, input_fn), fmt="qe/cp/traj")
+                all_sys.append(sys)
+        sys_data_path = os.path.join(work_path, f"data.{ss}")
+        all_sys.to_deepmd_raw(sys_data_path)
+        all_sys.to_deepmd_npy(sys_data_path, set_size=len(sys_output), prec=np.float64)
+
+
 def post_fp_custom(iter_index, jdata):
     """Post fp for custom fp. Collect data from user-defined `output_fn`.
 
@@ -4813,6 +4920,8 @@ def post_fp(iter_index, jdata):
         post_fp_pwmat(iter_index, jdata)
     elif fp_style == "amber/diff":
         post_fp_amber_diff(iter_index, jdata)
+    elif fp_style == "cpx":
+        post_fp_cpx(iter_index, jdata)
     elif fp_style == "custom":
         post_fp_custom(iter_index, jdata)
     else:

examples/qe-cpx/POSCAR_SiO2-phosph

@@ -0,0 +1,78 @@
+PSiO2 70 atoms
+1.0
+9.712 0.0   0.0
+0.0   7.284 0.0
+0.0   0.0   25.0
+Si  O   P
+18  36  16
+Cartesian
+0.0  2.280860772  8.54401772
+2.5751368  1.287570828  6.77198228
+2.2808631999999998  3.7155684  5.0
+0.0  7.1368632  8.54401772
+2.5751368  6.143565971999999  6.77198228
+7.1368632  1.287570828  5.0
+4.856  4.708865628  8.54401772
+7.4311368  3.7155684  6.77198228
+7.1368632  6.143565971999999  5.0
+0.0  2.280860772  13.86001772
+2.5751368  1.287570828  12.087982279999999
+2.2808631999999998  3.7155684  10.315999999999999
+0.0  7.1368632  13.86001772
+2.5751368  6.143565971999999  12.087982279999999
+7.1368632  1.287570828  10.315999999999999
+4.856  4.708865628  13.86001772
+7.4311368  3.7155684  12.087982279999999
+7.1368632  6.143565971999999  10.315999999999999
+2.0069848  0.2940310428  5.6315408
+4.1465384  0.7757459999999999  7.403523079999999
+1.2975231999999999  1.358225628  7.91247692
+0.7094616  3.2037435719999996  9.6844592
+2.8490151999999997  2.7220307999999998  6.14044148
+5.565461599999999  0.7757459999999999  9.6844592
+7.7050152  0.2940310428  6.14044148
+2.0069848  5.150028372  5.6315408
+3.5584767999999998  3.7862232000000002  9.17555852
+4.1465384  5.631748428  7.403523079999999
+1.2975231999999999  6.214220772  7.91247692
+6.8629847999999996  2.7220307999999998  5.6315408
+8.4144768  1.358225628  9.17555852
+9.0025384  3.2037435719999996  7.403523079999999
+6.1535232  3.7862232000000002  7.91247692
+5.565461599999999  5.631748428  9.6844592
+7.7050152  5.150028372  6.14044148
+8.4144768  6.214220772  9.17555852
+2.0069848  0.2940310428  10.947540799999999
+4.1465384  0.7757459999999999  12.719523079999998
+1.2975231999999999  1.358225628  13.22847692
+0.7094616  3.2037435719999996  15.0004592
+2.8490151999999997  2.7220307999999998  11.45644148
+5.565461599999999  0.7757459999999999  15.0004592
+7.7050152  0.2940310428  11.45644148
+2.0069848  5.150028372  10.947540799999999
+3.5584767999999998  3.7862232000000002  14.49155852
+4.1465384  5.631748428  12.719523079999998
+1.2975231999999999  6.214220772  13.22847692
+6.8629847999999996  2.7220307999999998  10.947540799999999
+8.4144768  1.358225628  14.49155852
+9.0025384  3.2037435719999996  12.719523079999998
+6.1535232  3.7862232000000002  13.22847692
+5.565461599999999  5.631748428  15.0004592
+7.7050152  5.150028372  11.45644148
+8.4144768  6.214220772  14.49155852
+0.00476347936058176  0.0329022524829  18.956790026599506
+1.492078463890618  1.6780148766279  18.956795481599528
+2.2060016312005817  1.6780148766279  16.83262392826639
+3.6933254206832253  0.0329022524829  16.83262392826639
+4.407239783040581  0.0329022524829  18.956790026599506
+5.894554767570618  1.6780148766279  18.956795481599528
+6.608477934880581  1.6780148766279  16.83262392826639
+8.095801724363225  0.0329022524829  16.83262392826639
+0.00476347936058176  3.3231275007728995  18.956790026599506
+1.492078463890618  4.9682401249179  18.956795481599528
+2.2060016312005817  4.9682401249179  16.83262392826639
+3.6933254206832253  3.3231275007728995  16.83262392826639
+4.407239783040581  3.3231275007728995  18.956790026599506
+5.894554767570618  4.9682401249179  18.956795481599528
+6.608477934880581  4.9682401249179  16.83262392826639
+8.095801724363225  3.3231275007728995  16.83262392826639

examples/qe-cpx/POSCAR_phosphorene

@@ -0,0 +1,24 @@
+P16
+1.0
+8.8051536400000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+0.0000000000000000e+00 6.5802993500000000e+00 0.0000000000000000e+00
+0.0000000000000000e+00 0.0000000000000000e+00 2.1819520480000000e+01
+P
+16
+Cartesian
+   0.0047932879    0.0329221655   12.1379214560
+   1.4920806296    1.6779599686   12.1379256454
+   2.2061033938    1.6779553229   10.0134938897
+   3.6933908587    0.0329258241   10.0134877584
+   4.4073895408    0.0329264690   12.1379193395
+   5.8946802725    1.6779594027   12.1379136883
+   6.6086281312    1.6779562836   10.0134764995
+   8.0959086049    0.0329227774   10.0134900713
+   0.0048354294    3.3230308180   12.1379111354
+   1.4920256238    4.9681445314   12.1379043059
+   2.2061652764    4.9681443340   10.0134972717
+   3.6933414794    3.3230264750   10.0134912277
+   4.4074328798    3.3230248628   12.1379032804
+   5.8946135118    4.9681435707   12.1379085170
+   6.6086811470    4.9681455908   10.0134957444
+   8.0958607312    3.3230316405   10.0134979045

examples/qe-cpx/qe_template_P.in

@@ -0,0 +1,47 @@
+&CONTROL
+  calculation='cp',
+  restart_mode='from_scratch'
+  outdir='.',
+  prefix='P',
+  pseudo_dir='/your/path/to/pseudopotentials',
+  nstep=100,
+  iprint=100,
+  isave=200,
+  dt=5.0,
+  ndw=50,
+  tprnfor=.true.
+  tstress=.true.
+  etot_conv_thr=1.d-9
+  ekin_conv_thr=1.d-7
+/
+
+&SYSTEM
+  ibrav=0,
+  nat=16,
+  ntyp=1,
+  ecutwfc=60,
+  ecutrho=360,
+  nr1b=20, nr2b=20, nr3b=20,
+/
+
+&ELECTRONS
+  electron_dynamics='damp',
+  electron_damping=0.1,
+  emass=300,
+  orthogonalization='ortho',
+  ortho_eps=1d-11,
+  ortho_max=1000
+/
+
+&IONS
+  ion_dynamics='none'
+/
+
+ATOMIC_SPECIES
+  P 30.973762d0 P.pbesol-n-rrkjus_psl.1.0.0.UPF
+
+ATOMIC_POSITIONS {angstrom}
+%POSITIONS%
+
+CELL_PARAMETERS {angstrom}
+%CELL%