ipi 2.6.3__tar.gz → 3.0__tar.gz

{ipi-2.6.3 → ipi-3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipi
-Version: 2.6.3
+Version: 3.0
 Summary: A Python interface for ab initio path integral molecular dynamics simulations
 Home-page: http://ipi-code.org
 Author: The i-PI developers
@@ -45,6 +45,21 @@ and it implements most of the state-of-the-art methods to accelerate this kind o
 calculations. It has since grown to also provide all sorts of simulation 
 strategies, from replica exchange to geometry optimization. 
 
+If you use i-PI in your research, please cite the accompanying publication:
+for version 3, the relevant paper is 
+[Litman et al., *J. Chem. Phys.* 161, 062504 (2024)](https://doi.org/10.1063/5.0215869)
+
+```
+@article{litman2024ipi,
+title={i-PI 3.0: a flexible and efficient framework for advanced atomistic simulations},     
+author={Yair Litman and Venkat Kapil and Yotam M. Y. Feldman and Davide Tisi and Tomislav Begušić and Karen Fidanyan and Guillaume Fraux and Jacob Higer and Matthias Kellner and Tao E. Li and Eszter S. Pós and Elia Stocco and George Trenins and Barak Hirshberg and Mariana Rossi and Michele Ceriotti},
+journal = {J. Chem. Phys.},
+pages   = {062505},
+volume  = {161},
+year    = {2024}
+}
+```
+
 Quick Setup
 -----------
 
@@ -62,8 +77,8 @@ Last Release:
 pip install -U ipi
 ```
 
-Full installation
------------------
+Source installation
+-------------------
 
 To develop i-PI or test it with the self-contained driver, follow these
 instructions. It is assumed that i-PI will
@@ -111,8 +126,8 @@ else if you want to keep the i-PI directory clean. For example
 ```bash
 cd demos/para-h2-tutorial/tutorial-1/
 i-pi tutorial-1.xml > log &
-i-pi-driver -h localhost -p 31415 -m sg -o 15 &
-i-pi-driver -h localhost -p 31415 -m sg -o 15 &
+i-pi-driver -a localhost -p 31415 -m sg -o 15 &
+i-pi-driver -a localhost -p 31415 -m sg -o 15 &
 tail -f log
 ```
 

{ipi-2.6.3 → ipi-3.0}/README.md

@@ -17,6 +17,21 @@ and it implements most of the state-of-the-art methods to accelerate this kind o
 calculations. It has since grown to also provide all sorts of simulation 
 strategies, from replica exchange to geometry optimization. 
 
+If you use i-PI in your research, please cite the accompanying publication:
+for version 3, the relevant paper is 
+[Litman et al., *J. Chem. Phys.* 161, 062504 (2024)](https://doi.org/10.1063/5.0215869)
+
+```
+@article{litman2024ipi,
+title={i-PI 3.0: a flexible and efficient framework for advanced atomistic simulations},     
+author={Yair Litman and Venkat Kapil and Yotam M. Y. Feldman and Davide Tisi and Tomislav Begušić and Karen Fidanyan and Guillaume Fraux and Jacob Higer and Matthias Kellner and Tao E. Li and Eszter S. Pós and Elia Stocco and George Trenins and Barak Hirshberg and Mariana Rossi and Michele Ceriotti},
+journal = {J. Chem. Phys.},
+pages   = {062505},
+volume  = {161},
+year    = {2024}
+}
+```
+
 Quick Setup
 -----------
 
@@ -34,8 +49,8 @@ Last Release:
 pip install -U ipi
 ```
 
-Full installation
------------------
+Source installation
+-------------------
 
 To develop i-PI or test it with the self-contained driver, follow these
 instructions. It is assumed that i-PI will
@@ -83,8 +98,8 @@ else if you want to keep the i-PI directory clean. For example
 ```bash
 cd demos/para-h2-tutorial/tutorial-1/
 i-pi tutorial-1.xml > log &
-i-pi-driver -h localhost -p 31415 -m sg -o 15 &
-i-pi-driver -h localhost -p 31415 -m sg -o 15 &
+i-pi-driver -a localhost -p 31415 -m sg -o 15 &
+i-pi-driver -a localhost -p 31415 -m sg -o 15 &
 tail -f log
 ```
 

{ipi-2.6.3 → ipi-3.0}/bin/i-pi

@@ -58,7 +58,7 @@ def main(fn_input, options):
             raise ImportError('Profiling requires the `yappi` package.')            
 
     # construct simulation based on input file
-    simulation = Simulation.load_from_xml(fn_input, request_banner=True, custom_verbosity=options.verbosity)
+    simulation = Simulation.load_from_xml(fn_input, request_banner=True, custom_verbosity=options.verbosity, sockets_prefix=options.sockets_prefix)
 
     # run the simulation
     simulation.run()
@@ -96,6 +96,9 @@ if __name__ == '__main__':
                       choices=['quiet', 'low', 'medium', 'high', 'debug'],
                       help='Define the verbosity level.')
 
+    parser.add_option('-S', '--sockets_prefix', dest='sockets_prefix', default=None,
+                      help='Prefix for profiler files.')
+
     options, args = parser.parse_args()
 
     # make sure that we have exactly one input file and it exists

{ipi-2.6.3 → ipi-3.0}/bin/i-pi-committee-reweight

@@ -23,6 +23,7 @@ def direct_reweight(pot, obs, kbT):
     obs_avg_rew  : the observable reweighted for each potential
     weights      : the weights computed for each model and frame
     """
+
     beta = 1.0 / kbT
     num_pot_frames = pot.shape[0]
     num_obs_frames = obs.shape[0]
@@ -133,7 +134,7 @@ def uncertainty_CEA_multiple_models(pot, obs, kbT):
 
 
 def commitee_reweight(
-    path2ixml, pot_file, obs_file, stride=1, index=-1, direct=False, multi_models=False
+    pot_file, obs_file, kt, stride=1, index=-1, direct=False, multi_models=False
 ):
     """
     Parameters
@@ -145,6 +146,8 @@ def commitee_reweight(
                     A file containing the value of the observable for each frame.
                     It is assumed that lines correspond to frames, while columns to properties.
                     Multiple properties can be reweighted at the same time.
+    kt          :   float, mandatory
+                    The thermal energy, in the same units as pot_file
     stride      :   integer, [1]
                     The frequency of sampling of pot_file, if different from that of prop_file (e.g. --stride 10 if
                     the potential was printed 10 times more often than the observable. --stride -10 must be used if
@@ -175,15 +178,9 @@ def commitee_reweight(
     else:
         raise ValueError("Stride value cannot be zero")
 
-    # Load kbT from i-PI, we could make it into a small function
-    simul = Simulation.load_from_xml(
-        path2ixml, custom_verbosity="quiet", read_only=True
-    )
-    kbT = float(simul.syslist[0].ensemble.temp)
-
     if multi_models:
         mean_value, sigma2_a, sigma2_aV, sigma2_tilde = uncertainty_CEA_multiple_models(
-            potentials, obs, kbT
+            potentials, obs, kt
         )
         print("#     Mean            Error         sigma_a        sigma_aV")
         print(
@@ -194,9 +191,9 @@ def commitee_reweight(
     else:
         # CEA is the default choice. The weights or h_matrix are
         if direct:
-            rw_obs, _weights = direct_reweight(potentials, obs, kbT)
+            rw_obs, _weights = direct_reweight(potentials, obs, kt)
         else:
-            rw_obs, _h_matrix = CEA(potentials, obs, kbT)
+            rw_obs, _h_matrix = CEA(potentials, obs, kt)
         print(
             "#     Mean            Error        <committee_1>         ....         <committee_N>"
         )
@@ -215,21 +212,28 @@ if __name__ == "__main__":
     The full methodology is described in: https://doi.org/10.1063/5.0036522"""
     )
 
-    parser.add_argument(
-        "input_xml",
-        type=str,
-        help="The path to the input file used to run the simulation (usually input.xml)",
-    )
     parser.add_argument(
         "pot_file",
         type=str,
-        help="The file containing the potentials. Rows = frames, columns = potentials",
+        help="The file containing the potentials, in units of kT (default: Hartree). Rows = frames, columns = potentials",
     )
     parser.add_argument(
         "obs_file",
         type=str,
         help="The file containing the properties. Rows = frames, columns = property/ies",
     )
+    parser.add_argument(
+        "--kt",
+        type=float,
+        default=0.0,
+        help="The thermal energy. Should be in the same units of the potentials, typically Hartree",
+    )
+    parser.add_argument(
+        "--input",
+        type=str,
+        default="",
+        help="The path to the input file used to run the simulation (usually input.xml). Used just to extract kT.",
+    )
     parser.add_argument(
         "--stride",
         type=int,
@@ -254,11 +258,23 @@ if __name__ == "__main__":
     )
 
     args = parser.parse_args()
+
+    # Load kbT from i-PI, we could make it into a small function
+    if args.input != "":
+        simul = Simulation.load_from_xml(
+            args.input, custom_verbosity="quiet", read_only=True
+        )
+        kt = float(simul.syslist[0].ensemble.temp)
+    else:
+        kt = args.kt
+    if kt <= 0:
+        raise ValueError("Must specify either --kt or --input")
+
     sys.exit(
         commitee_reweight(
-            args.input_xml,
             args.pot_file,
             args.obs_file,
+            kt,
             args.stride,
             args.index,
             args.direct,

{ipi-2.6.3 → ipi-3.0}/bin/i-pi-driver-py

@@ -59,14 +59,19 @@ def Message(mystr):
 
 
 def run_driver(
-    unix=False, address="", port=12345, driver=Dummy_driver(), f_verbose=False
+    unix=False,
+    address="",
+    port=12345,
+    driver=Dummy_driver(),
+    f_verbose=False,
+    sockets_prefix="/tmp/ipi_",
 ):
     """Minimal socket client for i-PI."""
 
     # Opens a socket to i-PI
     if unix:
         sock = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
-        sock.connect("/tmp/ipi_" + address)
+        sock.connect(sockets_prefix + address)
     else:
         sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
         # this reduces latency for the small messages passed by the i-PI protocol
@@ -181,6 +186,13 @@ if __name__ == "__main__":
         default="localhost",
         help="Host name (for INET sockets) or name of the UNIX domain socket to connect to.",
     )
+    parser.add_argument(
+        "-S",
+        "--sockets_prefix",
+        type=str,
+        default="/tmp/ipi_",
+        help="Prefix used for the unix domain sockets. Ignored when using TCP/IP sockets.",
+    )
     parser.add_argument(
         "-p",
         "--port",
@@ -228,4 +240,5 @@ if __name__ == "__main__":
         port=args.port,
         driver=d_f,
         f_verbose=args.verbose,
+        sockets_prefix=args.sockets_prefix,
     )

{ipi-2.6.3 → ipi-3.0}/bin/i-pi-py_driver

@@ -59,14 +59,19 @@ def Message(mystr):
 
 
 def run_driver(
-    unix=False, address="", port=12345, driver=Dummy_driver(), f_verbose=False
+    unix=False,
+    address="",
+    port=12345,
+    driver=Dummy_driver(),
+    f_verbose=False,
+    sockets_prefix="/tmp/ipi_",
 ):
     """Minimal socket client for i-PI."""
 
     # Opens a socket to i-PI
     if unix:
         sock = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
-        sock.connect("/tmp/ipi_" + address)
+        sock.connect(sockets_prefix + address)
     else:
         sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
         # this reduces latency for the small messages passed by the i-PI protocol
@@ -181,6 +186,13 @@ if __name__ == "__main__":
         default="localhost",
         help="Host name (for INET sockets) or name of the UNIX domain socket to connect to.",
     )
+    parser.add_argument(
+        "-S",
+        "--sockets_prefix",
+        type=str,
+        default="/tmp/ipi_",
+        help="Prefix used for the unix domain sockets. Ignored when using TCP/IP sockets.",
+    )
     parser.add_argument(
         "-p",
         "--port",
@@ -228,4 +240,5 @@ if __name__ == "__main__":
         port=args.port,
         driver=d_f,
         f_verbose=args.verbose,
+        sockets_prefix=args.sockets_prefix,
     )

{ipi-2.6.3 → ipi-3.0}/bin/i-pi-remdsort

@@ -140,8 +140,11 @@ def main(inputfile, prefix="SRT_"):
                                     }
                                 )
                             else:
-                                filename = filename + "_" + padb + "." + o.format
-                                ofilename = ofilename + "_" + padb + "." + o.format
+                                extension = o.format
+                                if extension == "ase":  # special case
+                                    extension = "extxyz"
+                                filename = filename + "_" + padb + "." + extension
+                                ofilename = ofilename + "_" + padb + "." + extension
                                 ntraj.append(
                                     {
                                         "filename": filename,
@@ -164,7 +167,10 @@ def main(inputfile, prefix="SRT_"):
                         filename = s.prefix + "_" + o.filename
                     else:
                         filename = o.filename
-                    filename = filename + "." + o.format
+                    extension = o.format
+                    if extension == "ase":  # special case
+                        extension = "extxyz"
+                    filename = filename + "." + extension
                     ofilename = prefix + filename
                     ntraj.append(
                         {

{ipi-2.6.3 → ipi-3.0}/drivers/py/driver.py

@@ -59,14 +59,19 @@ def Message(mystr):
 
 
 def run_driver(
-    unix=False, address="", port=12345, driver=Dummy_driver(), f_verbose=False
+    unix=False,
+    address="",
+    port=12345,
+    driver=Dummy_driver(),
+    f_verbose=False,
+    sockets_prefix="/tmp/ipi_",
 ):
     """Minimal socket client for i-PI."""
 
     # Opens a socket to i-PI
     if unix:
         sock = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
-        sock.connect("/tmp/ipi_" + address)
+        sock.connect(sockets_prefix + address)
     else:
         sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
         # this reduces latency for the small messages passed by the i-PI protocol
@@ -181,6 +186,13 @@ if __name__ == "__main__":
         default="localhost",
         help="Host name (for INET sockets) or name of the UNIX domain socket to connect to.",
     )
+    parser.add_argument(
+        "-S",
+        "--sockets_prefix",
+        type=str,
+        default="/tmp/ipi_",
+        help="Prefix used for the unix domain sockets. Ignored when using TCP/IP sockets.",
+    )
     parser.add_argument(
         "-p",
         "--port",
@@ -228,4 +240,5 @@ if __name__ == "__main__":
         port=args.port,
         driver=d_f,
         f_verbose=args.verbose,
+        sockets_prefix=args.sockets_prefix,
     )

{ipi-2.6.3 → ipi-3.0}/drivers/py/pes/__init__.py

@@ -2,6 +2,7 @@
 
 import pkgutil
 import importlib
+import traceback
 
 __all__ = []
 
@@ -11,7 +12,11 @@ __drivers__ = {}
 # Iterate through all modules in the current package folder
 for loader, module_name, is_pkg in pkgutil.iter_modules(__path__):
     # Import the module
-    module = importlib.import_module("." + module_name, __package__)
+    try:
+        module = importlib.import_module("." + module_name, __package__)
+    except Exception:
+        print(f"!! Could not import PES module {module_name} !!")
+        traceback.print_exc()
 
     # Get the driver class and name from the module
     driver_class = getattr(module, "__DRIVER_CLASS__", None)

{ipi-2.6.3 → ipi-3.0}/drivers/py/pes/ase.py

@@ -18,9 +18,9 @@ __DRIVER_CLASS__ = "ASEDriver"
 
 ERROR_MSG = """
 This ASE driver requires specification of and ASE calculator
-and an ASE-readable template file that describes the chemical makeup of the structure. 
+and an ASE-readable template file that describes the chemical makeup of the structure.
 
-Example: python driver.py -m ase -u -o template.xyz,model_parameters 
+Example: python driver.py -m ase -u -o template.xyz,model_parameters
 """
 
 

{ipi-2.6.3 → ipi-3.0}/drivers/py/pes/doubledoublewell.py

@@ -14,7 +14,6 @@ from ipi.utils import units
 __DRIVER_NAME__ = "double_double_well"
 __DRIVER_CLASS__ = "DDW_with_explicit_bath_driver"
 
-# np.set_printoptions(precision=14, suppress=True,threshold='nan',linewidth=1000)
 
 invcm2au = units.unit_to_internal("frequency", "inversecm", 1.0)
 A2au = units.unit_to_internal("length", "angstrom", 1.0)
@@ -54,16 +53,16 @@ class DDW_with_explicit_bath_driver(Dummy_driver):
         self.error_msg = """\nDW+explicit_bath driver expects 11 arguments.\n
         Example: python driver.py -m DoubleWell_with_explicit_bath -o wb1 (cm^-1) V1 (cm^-1) wb2 (cm^-1) V2 (cm^-1) coupling(au) mass delta(\AA) eta0  eps1 eps2  deltaQ omega_c(cm^-1)     \n
         python driver.py -m DoubleWell -o 500,2085,500,2085,0.1,1837,0.00,1,0,0,1,500\n"""
-        self.args = args
-        self.check_arguments()
+        super(DDW_with_explicit_bath_driver, self).__init__(
+            args, error_msg=self.error_msg
+        )
         self.init = False
 
     def check_arguments(self):
         """Function that checks the arguments required to run the driver"""
 
         try:
-            arglist = self.args.split(",")
-            param = list(map(float, arglist))
+            param = list(map(float, self.args))
             assert len(param) == 12
             wb1 = param[0] * invcm2au
             v1 = param[1] * invcm2au
@@ -109,8 +108,6 @@ class DDW_with_explicit_bath_driver(Dummy_driver):
         y = pos.reshape(-1, 1)[self.ndof // 2 + 1 :]
         assert self.ndof == q1.size + q2.size + x.size + y.size
 
-        # fq1 = np.zeros(q1.shape)
-        # fq2 = np.zeros(q2.shape)
         fx = np.zeros(x.shape)
         fy = np.zeros(x.shape)
 

{ipi-2.6.3 → ipi-3.0}/drivers/py/pes/doublewell.py

@@ -15,8 +15,6 @@ __DRIVER_NAME__ = "DW"
 __DRIVER_CLASS__ = "DoubleWell_driver"
 
 
-# np.set_printoptions(precision=14, suppress=True,threshold='nan',linewidth=1000)
-
 invcm2au = units.unit_to_internal("frequency", "inversecm", 1.0)
 A2au = units.unit_to_internal("length", "angstrom", 1.0)
 
@@ -33,7 +31,7 @@ class DoubleWell_driver(Dummy_driver):
     def __init__(self, args=None, verbose=None):
         self.error_msg = """\nDW driver accepts 0 or 4 arguments.\nExample: python driver.py -m DoubleWell -o omega_b (cm^-1) V0 (cm^-1) mass(a.u) delta(angs) \n
         python driver.py -m DoubleWell -o 500,2085,1837,0.00 \n"""
-        super(DoubleWell_driver, self).__init__(args)
+        super(DoubleWell_driver, self).__init__(args, error_msg=self.error_msg)
 
     def check_arguments(self):
         """Function that checks the arguments required to run the driver"""
@@ -46,8 +44,7 @@ class DoubleWell_driver(Dummy_driver):
             self.delta = 00
         else:
             try:
-                arglist = self.args.split(",")
-                param = list(map(float, arglist))
+                param = list(map(float, self.args))
                 assert len(param) == 4
                 w_b = param[0] * invcm2au
                 v0 = param[1] * invcm2au

{ipi-2.6.3 → ipi-3.0}/drivers/py/pes/doublewell_with_bath.py

@@ -16,7 +16,6 @@ from ipi.utils import units
 __DRIVER_NAME__ = "DW_bath"
 __DRIVER_CLASS__ = "DoubleWell_with_explicit_bath_driver"
 
-# np.set_printoptions(precision=14, suppress=True,threshold='nan',linewidth=1000)
 
 invcm2au = units.unit_to_internal("frequency", "inversecm", 1.0)
 A2au = units.unit_to_internal("length", "angstrom", 1.0)
@@ -44,16 +43,17 @@ class DoubleWell_with_explicit_bath_driver(Dummy_driver):
         self.error_msg = """\nDW+explicit_bath driver expects 9 arguments.\n
         Example: python driver.py -m DoubleWell_with_explicit_bath -o omega_b (cm^-1) V0 (cm^-1) mass delta(\AA) eta0  eps1 eps2  deltaQ omega_c(cm^-1)     \n
         python driver.py -m DoubleWell -o 500,2085,1837,0.00,1,0,0,1,500\n"""
-        self.args = args
-        self.check_arguments()
+        super(DoubleWell_with_explicit_bath_driver, self).__init__(
+            args, error_msg=self.error_msg
+        )
+
         self.init = False
 
     def check_arguments(self):
         """Function that checks the arguments required to run the driver"""
 
         try:
-            arglist = self.args.split(",")
-            param = list(map(float, arglist))
+            param = list(map(float, self.args))
             assert len(param) == 9
             w_b = param[0] * invcm2au
             v0 = param[1] * invcm2au
@@ -62,7 +62,7 @@ class DoubleWell_with_explicit_bath_driver(Dummy_driver):
 
             self.bath_parameters = {}
             self.bath_parameters["m"] = param[2]
-            # self.bath_parameters["delta"] = param[3] * A2au
+
             self.bath_parameters["eta0"] = param[4]
             self.bath_parameters["eps1"] = param[5]
             self.bath_parameters["eps2"] = param[6]

{ipi-2.6.3 → ipi-3.0}/drivers/py/pes/doublewell_with_friction.py

@@ -15,7 +15,6 @@ import json
 __DRIVER_NAME__ = "DW_friction"
 __DRIVER_CLASS__ = "DoubleWell_with_friction_driver"
 
-# np.set_printoptions(precision=14, suppress=True,threshold='nan',linewidth=1000)
 
 invcm2au = units.unit_to_internal("frequency", "inversecm", 1.0)
 A2au = units.unit_to_internal("length", "angstrom", 1.0)
@@ -42,7 +41,8 @@ class DoubleWell_with_friction_driver(DoubleWell_driver):
         self.error_msg = """\nDW+fric driver expects 8 arguments.\n
         Example: python driver.py -m DoubleWell_with_fric -o omega_b (cm^-1) V0 (cm^-1) mass delta(\AA) eta0  eps1 eps2  deltaQ      \n
         python driver.py -m DoubleWell -o 500,2085,1837,0.00,1,0,0,1\n"""
-        self.args = args
+        self.args = args.split(",")
+        self.verbose = verbose
         self.check_arguments()
 
     def check_arguments(self):
@@ -50,8 +50,7 @@ class DoubleWell_with_friction_driver(DoubleWell_driver):
 
         self.k = 1837.36223469 * (3800.0 / 219323.0) ** 2
         try:
-            arglist = self.args.split(",")
-            param = list(map(float, arglist))
+            param = list(map(float, self.args))
             assert len(param) == 8
             w_b = param[0] * invcm2au
             v0 = param[1] * invcm2au