added ABACUS interface for first principle calculations (#433)

* delete unnecessary files

* remove ABACUS codes in relabel.py, fix test files.

* Add files via upload

* Add files via upload

Co-authored-by: LiuRenxi <LiuRenxi@MacBook-Air.local>

dpgen/generator/lib/abacus_pw_scf.py

@@ -0,0 +1,95 @@
+import numpy as np
+bohr2ang = 0.52917721067
+def make_abacus_pw_scf_kpt(fp_params):
+    # Make KPT file for abacus pw scf calculation.
+    # KPT file is the file containing k points infomation in ABACUS scf calculation.
+    k_points = [1, 1, 1, 0, 0, 0]
+    if "k_points" in fp_params:
+        k_points = fp_params["k_points"]
+        if len(k_points) != 6:
+            raise RuntimeError("k_points has to be a list containig 6 integers specifying MP k points generation.")
+    ret = "K_POINTS\n0\nGamma\n"
+    for i in range(6):
+        ret += str(k_points[i]) + " "
+    return ret
+
+def make_abacus_pw_scf_input(fp_params):
+    # Make INPUT file for abacus pw scf calculation.
+    ret = "INPUT_PARAMETERS\n"
+    assert(fp_params['ntype'] >= 0 and type(fp_params["ntype"]) == int)
+    ret += "ntype %d\n" % fp_params['ntype']
+    ret += "pseudo_dir ./\n"
+    if "ecutwfc" in fp_params:
+        assert(fp_params["ecutwfc"] >= 0)
+        ret += "ecutwfc %f\n" % fp_params["ecutwfc"]
+    if "mixing_type" in fp_params:
+        assert(fp_params["mixing_type"] in ["plain", "kerker", "pulay", "pulay-kerker", "broyden"])
+        ret += "mixing_type %s\n" % fp_params["mixing_type"]
+    if "mixing_beta" in fp_params:
+        assert(fp_params["mixing_beta"] >= 0 and fp_params["mixing_beta"] < 1)
+        ret += "mixing_beta %f\n" % fp_params["mixing_beta"]
+    if "symmetry" in fp_params:
+        assert(fp_params["symmetry"] == 0 or fp_params["symmetry"] == 1)
+        ret += "symmetry %d\n" % fp_params["symmetry"]
+    if "nbands" in fp_params:
+        assert(fp_params["nbands"] > 0 and type(fp_params["nbands"]) == int)
+        ret += "nbands %f\n" % fp_params["nbands"]
+    if "nspin" in fp_params:
+        assert(fp_params["nspin"] == 1 or fp_params["nspin"] == 2 or fp_params["nspin"] == 4)
+        ret += "nspin %d\n" % fp_params["nspin"]
+    if "ks_solver" in fp_params:
+        assert(fp_params["ks_solver"] in ["cg", "dav", "lapack", "genelpa", "hpseps", "scalapack_gvx"])
+        ret += "ks_solver %s\n" % fp_params["ks_solver"]
+    if "smearing" in fp_params:
+        assert(fp_params["smearing"] in ["gauss", "fd", "fixed", "mp", "mp2", "mv"])
+        ret += "smearing %s\n" % fp_params["smearing"]
+    if "sigma" in fp_params:
+        assert(fp_params["sigma"] >= 0)
+        ret += "sigma %f\n" % fp_params["sigma"]
+    ret += "force 1\nstress 1\n"
+    return ret
+
+def make_abacus_pw_scf_stru(sys_data, fp_pp_files):
+    atom_names = sys_data['atom_names']
+    atom_numbs = sys_data['atom_numbs']
+    assert(len(atom_names) == len(fp_pp_files))
+    assert(len(atom_names) == len(atom_numbs))
+    cell = sys_data["cells"][0].reshape([3, 3])
+    coord = sys_data['coords'][0]
+    #volume = np.linalg.det(cell)
+    #lattice_const = np.power(volume, 1/3)
+    lattice_const = 1/bohr2ang # in Bohr, in this way coord and cell are in Angstrom 
+
+    ret = "ATOMIC_SPECIES\n"
+    for iatom in range(len(atom_names)):
+        ret += atom_names[iatom] + " 1.00 " + fp_pp_files[iatom] + "\n"
+
+    ret += "\nLATTICE_CONSTANT\n"
+    ret += str(lattice_const) + "\n\n"
+
+    ret += "LATTICE_VECTORS\n"
+    for ix in range(3):
+        for iy in range(3):
+            ret += str(cell[ix][iy]) + " "
+        ret += "\n"
+    ret += "\n"
+
+    ret += "ATOMIC_POSITIONS\n"
+    ret += "Cartesian    # Cartesian(Unit is LATTICE_CONSTANT)\n"
+    natom_tot = 0
+    for iele in range(len(atom_names)):
+        ret += atom_names[iele] + "\n"
+        ret += "0.0\n"
+        ret += str(atom_numbs[iele]) + "\n"
+        for iatom in range(atom_numbs[iele]):
+            ret += "%.12f %.12f %.12f %d %d %d\n" % (coord[natom_tot, 0], coord[natom_tot, 1], coord[natom_tot, 2], 0, 0, 0)
+            natom_tot += 1
+    assert(natom_tot == sum(atom_numbs))
+
+    return ret
+
+
+if __name__ == "__main__":
+    fp_params = {"k_points": [1, 1, 1, 0, 0, 0]}
+    ret = make_abacus_pw_scf_kpt(fp_params)
+    print(ret)

dpgen/generator/run.py

@@ -43,6 +43,7 @@
 from dpgen.generator.lib.vasp import make_vasp_incar_user_dict
 from dpgen.generator.lib.vasp import incar_upper
 from dpgen.generator.lib.pwscf import make_pwscf_input
+from dpgen.generator.lib.abacus_pw_scf import make_abacus_pw_scf_stru, make_abacus_pw_scf_input, make_abacus_pw_scf_kpt
 #from dpgen.generator.lib.pwscf import cvt_1frame
 from dpgen.generator.lib.pwmat import make_pwmat_input_dict
 from dpgen.generator.lib.pwmat import write_input_dict
@@ -1795,6 +1796,41 @@ def make_fp_pwscf(iter_index,
     # link pp files
     _link_fp_vasp_pp(iter_index, jdata)
 
+def make_fp_abacus_pw_scf(iter_index,
+                  jdata) :
+    # make config
+    fp_tasks = _make_fp_vasp_configs(iter_index, jdata)
+    if len(fp_tasks) == 0 :
+        return
+    # make abacus/pw/scf input
+    iter_name = make_iter_name(iter_index)
+    work_path = os.path.join(iter_name, fp_name)
+    fp_pp_files = jdata['fp_pp_files']
+    if 'user_fp_params' in jdata.keys() :
+        fp_params = jdata['user_fp_params']
+        #user_input = True
+    else:
+        raise RuntimeError("Key 'user_fp_params' and its value have to be specified in parameter json file.")
+    cwd = os.getcwd()
+    for ii in fp_tasks:
+        os.chdir(ii)
+        sys_data = dpdata.System('POSCAR').data
+        if 'mass_map' in jdata:
+            sys_data['atom_masses'] = jdata['mass_map']
+        ret_input = make_abacus_pw_scf_input(fp_params)
+        with open('INPUT', 'w') as fp:
+            fp.write(ret_input)
+        ret_kpt = make_abacus_pw_scf_kpt(fp_params)
+        with open("KPT", "w") as fp:
+            fp.write(ret_kpt)
+        ret_stru = make_abacus_pw_scf_stru(sys_data, fp_pp_files)
+        with open("STRU", "w") as fp:
+            fp.write(ret_stru)
+
+        os.chdir(cwd)
+    # link pp files
+    _link_fp_vasp_pp(iter_index, jdata)
+
 
 def make_fp_siesta(iter_index,
                   jdata) :
@@ -1918,6 +1954,8 @@ def make_fp (iter_index,
         make_fp_vasp(iter_index, jdata)
     elif fp_style == "pwscf" :
         make_fp_pwscf(iter_index, jdata)
+    elif fp_style == "abacus/scf" :
+        make_fp_abacus_pw_scf(iter_index, jdata)
     elif fp_style == "siesta" :
         make_fp_siesta(iter_index, jdata)
     elif fp_style == "gaussian" :
@@ -1951,6 +1989,16 @@ def _qe_check_fin(ii) :
         return False
     return True
 
+def _abacus_pw_scf_check_fin(ii) :
+    if os.path.isfile(os.path.join(ii, 'OUT.ABACUS/running_scf.log')) :
+        with open(os.path.join(ii, 'OUT.ABACUS/running_scf.log'), 'r') as fp :
+            content = fp.read()
+            count = content.count('!FINAL_ETOT_IS')
+            if count != 1 :
+                return False
+    else :
+        return False
+    return True
 
 def _siesta_check_fin(ii) :
     if os.path.isfile(os.path.join(ii, 'output')) :
@@ -2061,6 +2109,10 @@ def run_fp (iter_index,
         forward_files = ['input'] + fp_pp_files
         backward_files = ['output']
         run_fp_inner(iter_index, jdata, mdata,  forward_files, backward_files, _qe_check_fin, log_file = 'output')
+    elif fp_style == "abacus/scf":
+        forward_files = ["INPUT", "STRU", "KPT"] + fp_pp_files
+        backward_files = ["output", "OUT.ABACUS"]
+        run_fp_inner(iter_index, jdata, mdata,  forward_files, backward_files, _abacus_pw_scf_check_fin, log_file = 'output')
     elif fp_style == "siesta":
         forward_files = ['input'] + fp_pp_files
         backward_files = ['output']
@@ -2235,6 +2287,51 @@ def post_fp_pwscf (iter_index,
         all_sys.to_deepmd_raw(sys_data_path)
         all_sys.to_deepmd_npy(sys_data_path, set_size = len(sys_output))
 
+def post_fp_abacus_pw_scf (iter_index,
+                        jdata):
+    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()
+
+    cwd = os.getcwd()
+    for ss in system_index :
+        sys_output = glob.glob(os.path.join(work_path, "task.%s.*"%ss))
+        sys_input = glob.glob(os.path.join(work_path, "task.%s.*/INPUT"%ss))
+        sys_output.sort()
+        sys_input.sort()
+
+        flag=True
+        for ii,oo in zip(sys_input,sys_output) :
+            if flag:
+                _sys = dpdata.LabeledSystem(oo, fmt = 'abacus/scf', type_map = jdata['type_map'])
+                if len(_sys)>0:
+                   all_sys=_sys
+                   flag=False
+                else:
+                   pass
+            else:
+                _sys = dpdata.LabeledSystem(oo, fmt = 'abacus/scf', type_map = jdata['type_map'])
+                if len(_sys)>0:
+                   all_sys.append(_sys)
+
+        sys_data_path = os.path.join(work_path, 'data.%s'%ss)
+        all_sys.to_deepmd_raw(sys_data_path)
+        all_sys.to_deepmd_npy(sys_data_path, set_size = len(sys_output))           
+
 def post_fp_siesta (iter_index,
                    jdata):
     model_devi_jobs = jdata['model_devi_jobs']
@@ -2424,6 +2521,8 @@ def post_fp (iter_index,
         post_fp_vasp(iter_index, jdata)
     elif fp_style == "pwscf" :
         post_fp_pwscf(iter_index, jdata)
+    elif fp_style == "abacus/scf":
+        post_fp_abacus_pw_scf(iter_index, jdata)
     elif fp_style == "siesta":
         post_fp_siesta(iter_index, jdata)
     elif fp_style == 'gaussian' :

dpgen/tools/relabel.py

@@ -202,7 +202,7 @@ def create_tasks(target_folder, param_file, output, fp_json, verbose = True, num
         copy_pp_files(output, fp_pp_path, fp_pp_files)
         make_vasp_incar(fp_params, output)
     if fp_style == 'pwscf' :
-        copy_pp_files(output, fp_pp_path, fp_pp_files)        
+        copy_pp_files(output, fp_pp_path, fp_pp_files)
     if fp_style == 'siesta' :
         copy_pp_files(output, fp_pp_path, fp_pp_files)
     for si in range(numb_sys) :

examples/run/dp1.x-lammps-ABACUS-pw/methane/machine.json

@@ -0,0 +1,88 @@
+{
+	"train":[
+	{
+	"machine":{
+		"machine_type": "slurm",
+		"host_name": "localhost",
+		"port": 22,
+		"username": "",
+		"work_path": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus"
+		},
+
+	"resources":{
+		"numb_node": 1,
+		"numb_gpu": 1,
+		"task_per_node": 1,
+		"partition": "",
+		"exclude_list": [],
+		"mem_limit": 0,
+		"source_list": ["/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/env.sh"],
+		"module_list": [],
+		"time_limit": "23:0:0",
+		"account":"",
+		"qos": ""	
+	},
+	"python_path": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_dpgen_interface/4_deepmd-kit/dpmd_install/bin/python"
+	}
+	],
+"model_devi": [
+	{
+		"machine": {	
+			"machine_type": "slurm",
+			"hostname": "localhost",
+			"port": 22,
+			"username": "",
+			"work_path": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus"	
+		},
+		"resources": {	
+			"num_node": 1,
+			"num_gpu": 0,
+			"task_per_node": 2,
+			"partition": "cn-large",
+			"exclude_list": [],
+			"mem_limit": 0,
+			"source_list": ["/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/env.sh"],
+			"module_list": [],
+			"time_limit": "14:00:00",
+			"account": "",
+			"qos": "",
+			"allow_failure":true
+		},
+		"command": "mpirun -n 2 lmp",
+		"group_size": 6
+	}
+],
+"fp": [
+	{
+		"machine":{
+			"machine_type": "slurm",
+			"hostname": "localhost",
+			"port": 22,
+			"username": "",
+			"work_path": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus"
+		},
+		"resources": {
+			"cvasp": false,
+			"numb_node": 1,
+			"partition": "cn-large",
+			"task_per_node": 4,
+
+			"numb_gpu": 0,
+			"exclude_list": [],
+			"with_mpi": false,
+			"mem_limit": 0,
+			"source_list":[
+				"/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/env.sh"
+			],
+			"module_list":[],
+			"time_limit": "48:0:0",
+			"account": "",
+			"qos": "",
+			"_comment": "that's all"
+		},
+		"command": "mpirun -np 4 ABACUS.mpi.2.1.0",
+		"group_size": 150
+	}
+
+]
+}