ipi 2.6.0__tar.gz → 3.0__tar.gz

{ipi-2.6.0 → ipi-3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipi
-Version: 2.6.0
+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
@@ -29,11 +29,11 @@ Requires-Dist: numpy
 i-PI: a Universal Force Engine
 ==============================
 
-A Python interface for ab initio path integral molecular dynamics simulations.
-i-PI is composed of a Python server (i-pi itself, that does not need to be
-compiled but only requires a relatively recent version of Python and Numpy)
-that apply an algorithm that updates the positions of the nuclei, and of an external
-code that acts as a client and computes the electronic energy and forces.
+A Python interface for ab initio path integral molecular dynamics simulations (and more).
+i-PI is a Python server (that does not need to be compiled and only requires a relatively 
+recent version of Python and Numpy) that applies an algorithm to update the positions of 
+the nuclei. One of many compatible external codes acts as client, and computes the 
+electronic energy and forces.
 
 This is typically a patched version of an electronic structure code, but a
 simple self-contained Fortran driver that implements several simple interatomic
@@ -45,29 +45,40 @@ 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. 
 
-Quick Setup and Test
---------------------
+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)
 
-To use i-PI with an existing driver, install and update using Pip:
+```
+@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
+-----------
+
+To use i-PI with an existing driver, install and update using `pip`:
+
+Last version:
 
-Last version::
 ```bash
 python -m pip install git+https://github.com/i-pi/i-pi.git
 ```
 
-Last Release::
-```bash
-pip install -U i-PI
-```
+Last Release:
 
-Test with Pytest::
 ```bash
-pip install pytest
-pytest --pyargs ipi.tests
+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
@@ -86,12 +97,17 @@ you always want to have i-PI available.
 
 ### Compile the driver code
 
+The built-in driver requires a FORTRAN compiler, and can be built as
+
 ```bash
 cd drivers/f90
 make
 cd ../..
 ```
 
+There is also a Python driver available in `drivers/py`, which however has limited
+functionalities. 
+
 ### Examples and demos
 
 The `examples` and `demos` folders contain inputs for many different types of
@@ -110,24 +126,25 @@ 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
 ```
 
 The monitoring can be interrupted with CTRL+C when the run has finished (5000 steps).
 
-
 ### Run the automatic test suite
 
-The automatic test suite can be run by calling the i-pi-test script.
+The automatic test suite can be run by calling the i-pi-tests script.
 You need to have the `pytest` package installed
 
 ```
-i-pi-test
+i-pi-tests
 ```
 
-See more details in the README file inside the ipi_tests folder.
+You may also need to install some dependencies, listed in `requirements.txt`.
+
+See more details in the README file inside the `ipi_tests` folder.
 
 Contributing
 ------------

{ipi-2.6.0 → ipi-3.0}/README.md

@@ -1,11 +1,11 @@
 i-PI: a Universal Force Engine
 ==============================
 
-A Python interface for ab initio path integral molecular dynamics simulations.
-i-PI is composed of a Python server (i-pi itself, that does not need to be
-compiled but only requires a relatively recent version of Python and Numpy)
-that apply an algorithm that updates the positions of the nuclei, and of an external
-code that acts as a client and computes the electronic energy and forces.
+A Python interface for ab initio path integral molecular dynamics simulations (and more).
+i-PI is a Python server (that does not need to be compiled and only requires a relatively 
+recent version of Python and Numpy) that applies an algorithm to update the positions of 
+the nuclei. One of many compatible external codes acts as client, and computes the 
+electronic energy and forces.
 
 This is typically a patched version of an electronic structure code, but a
 simple self-contained Fortran driver that implements several simple interatomic
@@ -17,29 +17,40 @@ 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. 
 
-Quick Setup and Test
---------------------
+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)
 
-To use i-PI with an existing driver, install and update using Pip:
+```
+@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
+-----------
+
+To use i-PI with an existing driver, install and update using `pip`:
+
+Last version:
 
-Last version::
 ```bash
 python -m pip install git+https://github.com/i-pi/i-pi.git
 ```
 
-Last Release::
-```bash
-pip install -U i-PI
-```
+Last Release:
 
-Test with Pytest::
 ```bash
-pip install pytest
-pytest --pyargs ipi.tests
+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
@@ -58,12 +69,17 @@ you always want to have i-PI available.
 
 ### Compile the driver code
 
+The built-in driver requires a FORTRAN compiler, and can be built as
+
 ```bash
 cd drivers/f90
 make
 cd ../..
 ```
 
+There is also a Python driver available in `drivers/py`, which however has limited
+functionalities. 
+
 ### Examples and demos
 
 The `examples` and `demos` folders contain inputs for many different types of
@@ -82,24 +98,25 @@ 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
 ```
 
 The monitoring can be interrupted with CTRL+C when the run has finished (5000 steps).
 
-
 ### Run the automatic test suite
 
-The automatic test suite can be run by calling the i-pi-test script.
+The automatic test suite can be run by calling the i-pi-tests script.
 You need to have the `pytest` package installed
 
 ```
-i-pi-test
+i-pi-tests
 ```
 
-See more details in the README file inside the ipi_tests folder.
+You may also need to install some dependencies, listed in `requirements.txt`.
+
+See more details in the README file inside the `ipi_tests` folder.
 
 Contributing
 ------------

{ipi-2.6.0 → ipi-3.0}/bin/i-pi

@@ -34,7 +34,7 @@ def profile_exit(prefix="profile"):
     # write out the outputs of the profiler
     import yappi            
     yappi.stop()
-    yappi.get_thread_stats().print_all()
+    #yappi.get_thread_stats().print_all()
     yfs = yappi.get_func_stats()
     yfs.save(prefix+".kgrind", type="callgrind")
     ypo = open(prefix+".yappi", "w")
@@ -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-2.6.0 → 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-3.0/bin/i-pi-driver-py

@@ -0,0 +1,244 @@
+#!/usr/bin/env python3
+import socket
+import argparse
+import numpy as np
+
+
+try:
+    from pes import *
+except ImportError:
+    # when in an installed i-PI package
+    from ipi._driver.pes import *
+
+description = """
+Minimal example of a Python driver connecting to i-PI and exchanging energy, forces, etc.
+"""
+
+
+def recv_data(sock, data):
+    """Fetches binary data from i-PI socket."""
+    blen = data.itemsize * data.size
+    buf = np.zeros(blen, np.byte)
+
+    bpos = 0
+    while bpos < blen:
+        timeout = False
+        try:
+            bpart = 1
+            bpart = sock.recv_into(buf[bpos:], blen - bpos)
+        except socket.timeout:
+            print(" @SOCKET:   Timeout in status recvall, trying again!")
+            timeout = True
+            pass
+        if not timeout and bpart == 0:
+            raise RuntimeError("Socket disconnected!")
+        bpos += bpart
+    if np.isscalar(data):
+        return np.frombuffer(buf[0:blen], data.dtype)[0]
+    else:
+        return np.frombuffer(buf[0:blen], data.dtype).reshape(data.shape)
+
+
+def send_data(sock, data):
+    """Sends binary data to i-PI socket."""
+
+    if np.isscalar(data):
+        data = np.array([data], data.dtype)
+    buf = data.tobytes()
+    sock.send(buf)
+
+
+HDRLEN = 12  # number of characters of the default message strings
+
+
+def Message(mystr):
+    """Returns a header of standard length HDRLEN."""
+
+    # convert to bytestream since we'll be sending this over a socket
+    return str.ljust(str.upper(mystr), HDRLEN).encode()
+
+
+def run_driver(
+    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(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
+        sock.setsockopt(socket.IPPROTO_TCP, socket.TCP_NODELAY, 1)
+        sock.connect((address, port))
+
+    f_init = False
+    f_data = False
+
+    # initializes structure arrays
+    cell = np.zeros((3, 3), float)
+    icell = np.zeros((3, 3), float)
+    pos = np.zeros(0, float)
+
+    # initializes return arrays
+    pot = 0.0
+    force = np.zeros(0, float)
+    vir = np.zeros((3, 3), float)
+    while True:  # ah the infinite loop!
+        header = sock.recv(HDRLEN)
+        if f_verbose:
+            print("Received ", header)
+        if header == Message("STATUS"):
+            # responds to a status request
+            if not f_init:
+                sock.sendall(Message("NEEDINIT"))
+            elif f_data:
+                sock.sendall(Message("HAVEDATA"))
+            else:
+                sock.sendall(Message("READY"))
+        elif header == Message("INIT"):
+            # initialization
+            rid = recv_data(sock, np.int32())
+            initlen = recv_data(sock, np.int32())
+            initstr = recv_data(sock, np.chararray(initlen))
+            if f_verbose:
+                print(rid, initstr)
+            f_init = True  # we are initialized now
+        elif header == Message("POSDATA"):
+            # receives structural information
+            cell = recv_data(sock, cell)
+            icell = recv_data(
+                sock, icell
+            )  # inverse of the cell. mostly useless legacy stuff
+            nat = recv_data(sock, np.int32())
+            if len(pos) == 0:
+                # shapes up the position array
+                pos.resize((nat, 3))
+                force.resize((nat, 3))
+            else:
+                if len(pos) != nat:
+                    raise RuntimeError("Atom number changed during i-PI run")
+            pos = recv_data(sock, pos)
+
+            ##### THIS IS THE TIME TO DO SOMETHING WITH THE POSITIONS!
+            pot, force, vir, extras = driver(cell, pos)
+            f_data = True
+        elif header == Message("GETFORCE"):
+            sock.sendall(Message("FORCEREADY"))
+
+            # sanity check in the returned values (catches bugs and inconsistencies in the implementation)
+            if not isinstance(force, np.ndarray) and force.dtype == np.float64:
+                raise ValueError(
+                    "driver returned forces with the wrong type: we need a "
+                    "numpy.ndarray containing 64-bit floating points values"
+                )
+
+            if not isinstance(vir, np.ndarray) and vir.dtype == np.float64:
+                raise ValueError(
+                    "driver returned virial with the wrong type: we need a "
+                    "numpy.ndarray containing 64-bit floating points values"
+                )
+
+            if len(force.flatten()) != len(pos.flatten()):
+                raise ValueError(
+                    "driver returned forces with the wrong size: number of "
+                    "atoms and dimensions must match positions"
+                )
+
+            if len(vir.flatten()) != 9:
+                raise ValueError(
+                    "driver returned a virial tensor which does not have 9 components"
+                )
+
+            send_data(sock, np.float64(pot))
+            send_data(sock, np.int32(nat))
+            send_data(sock, force)
+            send_data(sock, vir)
+            send_data(sock, np.int32(len(extras)))
+            sock.sendall(extras.encode("utf-8"))
+
+            f_data = False
+        elif header == Message("EXIT"):
+            print("Received exit message from i-PI. Bye bye!")
+            return
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description=description)
+
+    parser.add_argument(
+        "-u",
+        "--unix",
+        action="store_true",
+        default=False,
+        help="Use a UNIX domain socket.",
+    )
+    parser.add_argument(
+        "-a",
+        "--address",
+        type=str,
+        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",
+        type=int,
+        default=12345,
+        help="TCP/IP port number. Ignored when using UNIX domain sockets.",
+    )
+    parser.add_argument(
+        "-m",
+        "--mode",
+        type=str,
+        default="dummy",
+        help="""Type of potential to be used to compute the potential and its derivatives.
+                Currently implemented: [dummy, harmonic]
+        """,
+    )
+    parser.add_argument(
+        "-o",
+        "--param",
+        type=str,
+        default="",
+        help="""Parameters required to run the driver. Comma-separated list of values
+        """,
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="store_true",
+        default=False,
+        help="Verbose output.",
+    )
+
+    args = parser.parse_args()
+
+    if args.mode in __drivers__:
+        d_f = __drivers__[args.mode](args.param, args.verbose)
+    elif args.mode == "dummy":
+        d_f = Dummy_driver(args.param, args.verbose)
+    else:
+        raise ValueError("Unsupported driver mode ", args.mode)
+
+    run_driver(
+        unix=args.unix,
+        address=args.address,
+        port=args.port,
+        driver=d_f,
+        f_verbose=args.verbose,
+        sockets_prefix=args.sockets_prefix,
+    )

{ipi-2.6.0 → ipi-3.0}/bin/i-pi-planetary

@@ -189,7 +189,6 @@ def simple_corr(A, B, **kwargs):
 
 
 class Planets(object):
-
     """
     Stores relevant trajectory info for planetary model simulation, calculates
     planetary dynamics and evaluates estimators and TCFs.