Merge branch 'lammps:develop' into master
This commit is contained in:
Evangelos Voyiatzis
@ -168,7 +168,7 @@ OPT.
|
||||
* :doc:`pafi <fix_pafi>`
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* :doc:`pair <fix_pair>`
|
||||
* :doc:`phonon <fix_phonon>`
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* :doc:`pimd <fix_pimd>`
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* :doc:`pimd/nvt <fix_pimd>`
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||||
* :doc:`planeforce <fix_planeforce>`
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||||
* :doc:`plumed <fix_plumed>`
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||||
* :doc:`poems <fix_poems>`
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|
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@ -451,7 +451,10 @@ piece of python code:
|
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for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
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if (j>=j1): print j1/2.,j2/2.,j/2.
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|
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For even twojmax = 2(*m*\ -1), :math:`K = m(m+1)(2m+1)/6`, the *m*\ -th pyramidal number. For odd twojmax = 2 *m*\ -1, :math:`K = m(m+1)(m+2)/3`, twice the *m*\ -th tetrahedral number.
|
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There are :math:`m(m+1)/2` descriptors with last index *j*,
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where *m* = :math:`\lfloor j \rfloor + 1`.
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Hence, for even *twojmax* = 2(*m*\ -1), :math:`K = m(m+1)(2m+1)/6`, the *m*\ -th pyramidal number,
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and for odd *twojmax* = 2 *m*\ -1, :math:`K = m(m+1)(m+2)/3`, twice the *m*\ -th tetrahedral number.
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.. note::
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@ -320,7 +320,7 @@ accelerated styles exist.
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* :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
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* :doc:`pair <fix_pair>` - access per-atom info from pair styles
|
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* :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
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* :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
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* :doc:`pimd/nvt <fix_pimd>` - Feynman path integral molecular dynamics with Nose-Hoover thermostat
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* :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
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* :doc:`plumed <fix_plumed>` - wrapper on PLUMED free energy library
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* :doc:`poems <fix_poems>` - constrain clusters of atoms to move as coupled rigid bodies
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@ -1,6 +1,6 @@
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.. index:: fix pimd
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.. index:: fix pimd/nvt
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fix pimd command
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fix pimd/nvt command
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================
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Syntax
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@ -8,10 +8,10 @@ Syntax
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.. parsed-literal::
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fix ID group-ID pimd keyword value ...
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fix ID group-ID pimd/nvt keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* pimd = style name of this fix command
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* pimd/nvt = style name of this fix command
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* zero or more keyword/value pairs may be appended
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* keyword = *method* or *fmass* or *sp* or *temp* or *nhc*
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@ -28,11 +28,15 @@ Examples
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.. code-block:: LAMMPS
|
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|
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fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
|
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fix 1 all pimd/nvt method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
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|
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Description
|
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"""""""""""
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.. versionchanged:: TBD
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Fix pimd was renamed to fix pimd/nvt.
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This command performs quantum molecular dynamics simulations based on
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the Feynman path integral to include effects of tunneling and
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zero-point motion. In this formalism, the isomorphism of a quantum
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@ -67,7 +71,7 @@ number of NH thermostats would be 3 x N x P x Nc.
|
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|
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.. note::
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|
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This fix implements a complete velocity-verlet integrator
|
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Fix pimd/nvt implements a complete velocity-verlet integrator
|
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combined with NH massive chain thermostat, so no other time
|
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integration fix should be used.
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|
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@ -76,31 +80,33 @@ value of *pimd* is standard PIMD. A value of *nmpimd* is for
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normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
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(CMD). The difference between the styles is as follows.
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In standard PIMD, the value used for a bead's fictitious mass is
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arbitrary. A common choice is to use Mi = m/P, which results in the
|
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mass of the entire ring-polymer being equal to the real quantum
|
||||
particle. But it can be difficult to efficiently integrate the
|
||||
equations of motion for the stiff harmonic interactions in the ring
|
||||
polymers.
|
||||
In standard PIMD, the value used for a bead's fictitious mass is
|
||||
arbitrary. A common choice is to use Mi = m/P, which results in the
|
||||
mass of the entire ring-polymer being equal to the real quantum
|
||||
particle. But it can be difficult to efficiently integrate the
|
||||
equations of motion for the stiff harmonic interactions in the ring
|
||||
polymers.
|
||||
|
||||
A useful way to resolve this issue is to integrate the equations of
|
||||
motion in a normal mode representation, using Normal Mode
|
||||
Path-Integral Molecular Dynamics (NMPIMD) :ref:`(Cao1) <Cao1>`. In NMPIMD,
|
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the NH chains are attached to each normal mode of the ring-polymer and
|
||||
the fictitious mass of each mode is chosen as Mk = the eigenvalue of
|
||||
the Kth normal mode for k > 0. The k = 0 mode, referred to as the
|
||||
zero-frequency mode or centroid, corresponds to overall translation of
|
||||
the ring-polymer and is assigned the mass of the real particle.
|
||||
A useful way to resolve this issue is to integrate the equations of
|
||||
motion in a normal mode representation, using Normal Mode
|
||||
Path-Integral Molecular Dynamics (NMPIMD) :ref:`(Cao1) <Cao1>`. In
|
||||
NMPIMD, the NH chains are attached to each normal mode of the
|
||||
ring-polymer and the fictitious mass of each mode is chosen as Mk =
|
||||
the eigenvalue of the Kth normal mode for k > 0. The k = 0 mode,
|
||||
referred to as the zero-frequency mode or centroid, corresponds to
|
||||
overall translation of the ring-polymer and is assigned the mass of
|
||||
the real particle.
|
||||
|
||||
Motion of the centroid can be effectively uncoupled from the other
|
||||
normal modes by scaling the fictitious masses to achieve a partial
|
||||
adiabatic separation. This is called a Centroid Molecular Dynamics
|
||||
(CMD) approximation :ref:`(Cao2) <Cao2>`. The time-evolution (and resulting
|
||||
dynamics) of the quantum particles can be used to obtain centroid time
|
||||
correlation functions, which can be further used to obtain the true
|
||||
quantum correlation function for the original system. The CMD method
|
||||
also uses normal modes to evolve the system, except only the k > 0
|
||||
modes are thermostatted, not the centroid degrees of freedom.
|
||||
Motion of the centroid can be effectively uncoupled from the other
|
||||
normal modes by scaling the fictitious masses to achieve a partial
|
||||
adiabatic separation. This is called a Centroid Molecular Dynamics
|
||||
(CMD) approximation :ref:`(Cao2) <Cao2>`. The time-evolution (and
|
||||
resulting dynamics) of the quantum particles can be used to obtain
|
||||
centroid time correlation functions, which can be further used to
|
||||
obtain the true quantum correlation function for the original system.
|
||||
The CMD method also uses normal modes to evolve the system, except
|
||||
only the k > 0 modes are thermostatted, not the centroid degrees of
|
||||
freedom.
|
||||
|
||||
The keyword *fmass* sets a further scaling factor for the fictitious
|
||||
masses of beads, which can be used for the Partial Adiabatic CMD
|
||||
@ -152,47 +158,47 @@ related tasks for each of the partitions, e.g.
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
This fix writes the state of the Nose/Hoover thermostat over all
|
||||
Fix pimd/nvt writes the state of the Nose/Hoover thermostat over all
|
||||
quasi-beads to :doc:`binary restart files <restart>`. See the
|
||||
:doc:`read_restart <read_restart>` command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file, so that the
|
||||
operation of the fix continues in an uninterrupted fashion.
|
||||
|
||||
None of the :doc:`fix_modify <fix_modify>` options
|
||||
are relevant to this fix.
|
||||
are relevant to fix pimd/nvt.
|
||||
|
||||
This fix computes a global 3-vector, which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The three quantities in the
|
||||
global vector are
|
||||
Fix pimd/nvt computes a global 3-vector, which can be accessed by
|
||||
various :doc:`output commands <Howto_output>`. The three quantities in
|
||||
the global vector are:
|
||||
|
||||
#. the total spring energy of the quasi-beads,
|
||||
#. the current temperature of the classical system of ring polymers,
|
||||
#. the current value of the scalar virial estimator for the kinetic
|
||||
energy of the quantum system :ref:`(Herman) <Herman>`.
|
||||
#. the total spring energy of the quasi-beads,
|
||||
#. the current temperature of the classical system of ring polymers,
|
||||
#. the current value of the scalar virial estimator for the kinetic
|
||||
energy of the quantum system :ref:`(Herman) <Herman>`.
|
||||
|
||||
The vector values calculated by this fix are "extensive", except for the
|
||||
The vector values calculated by fix pimd/nvt are "extensive", except for the
|
||||
temperature, which is "intensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during
|
||||
No parameter of fix pimd/nvt can be used with the *start/stop* keywords
|
||||
of the :doc:`run <run>` command. Fix pimd/nvt is not invoked during
|
||||
:doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix is part of the REPLICA package. It is only enabled if
|
||||
LAMMPS was built with that package. See the
|
||||
:doc:`Build package <Build_package>` page for more info.
|
||||
This fix is part of the REPLICA package. It is only enabled if LAMMPS
|
||||
was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
Fix pid cannot be used with :doc:`lj units <units>`.
|
||||
Fix pimd/nvt cannot be used with :doc:`lj units <units>`.
|
||||
|
||||
A PIMD simulation can be initialized with a single data file read via
|
||||
the :doc:`read_data <read_data>` command. However, this means all
|
||||
quasi-beads in a ring polymer will have identical positions and
|
||||
velocities, resulting in identical trajectories for all quasi-beads.
|
||||
To avoid this, users can simply initialize velocities with different
|
||||
random number seeds assigned to each partition, as defined by the
|
||||
uloop variable, e.g.
|
||||
velocities, resulting in identical trajectories for all quasi-beads. To
|
||||
avoid this, users can simply initialize velocities with different random
|
||||
number seeds assigned to each partition, as defined by the uloop
|
||||
variable, e.g.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
@ -201,8 +207,8 @@ uloop variable, e.g.
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0,
|
||||
and nhc = 2.
|
||||
The keyword defaults for fix pimd/nvt are method = pimd, fmass = 1.0, sp
|
||||
= 1.0, temp = 300.0, and nhc = 2.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -256,7 +256,7 @@ for command_type, entries in index.items():
|
||||
print("Total number of style index entries:", total_index)
|
||||
|
||||
skip_angle = ('sdk')
|
||||
skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
|
||||
skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species', 'pimd')
|
||||
skip_pair = ('meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm')
|
||||
skip_compute = ('pressure/cylinder')
|
||||
|
||||
@ -286,7 +286,7 @@ if counter:
|
||||
counter = 0
|
||||
|
||||
counter += check_style_index("compute", compute, index["compute"], skip=['pressure/cylinder'])
|
||||
counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
|
||||
counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species','pimd'])
|
||||
counter += check_style_index("angle_style", angle, index["angle_style"], skip=['sdk'])
|
||||
counter += check_style_index("bond_style", bond, index["bond_style"])
|
||||
counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
|
||||
|
||||
@ -17,7 +17,7 @@ timestep 0.001
|
||||
|
||||
velocity all create 1.0 1985 rot yes dist gaussian
|
||||
|
||||
fix 1 all pimd method nmpimd fmass 1.0 temp 25.0 nhc 4
|
||||
fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
|
||||
|
||||
thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
|
||||
thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
|
||||
|
||||
@ -17,7 +17,7 @@ read_data system.data
|
||||
#read_restart system_${ibead}.rest1
|
||||
special_bonds charmm
|
||||
|
||||
fix 1 all pimd method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
|
||||
fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3]
|
||||
|
||||
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -1533,6 +1533,8 @@
|
||||
/fix_mol_swap.h
|
||||
/fix_pimd.cpp
|
||||
/fix_pimd.h
|
||||
/fix_pimd_nvt.cpp
|
||||
/fix_pimd_nvt.h
|
||||
/fix_qbmsst.cpp
|
||||
/fix_qbmsst.h
|
||||
/fix_qtb.cpp
|
||||
|
||||
@ -185,17 +185,17 @@ void AngleTable::allocate()
|
||||
|
||||
void AngleTable::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR, "Illegal angle_style command");
|
||||
if (narg != 2) error->all(FLERR, "Illegal angle_style command: must have 2 arguments");
|
||||
|
||||
if (strcmp(arg[0], "linear") == 0)
|
||||
tabstyle = LINEAR;
|
||||
else if (strcmp(arg[0], "spline") == 0)
|
||||
tabstyle = SPLINE;
|
||||
else
|
||||
error->all(FLERR, "Unknown table style in angle style table");
|
||||
error->all(FLERR, "Unknown table style {} in angle style table", arg[0]);
|
||||
|
||||
tablength = utils::inumeric(FLERR, arg[1], false, lmp);
|
||||
if (tablength < 2) error->all(FLERR, "Illegal number of angle table entries");
|
||||
if (tablength < 2) error->all(FLERR, "Illegal number of angle table entries: {}", arg[1]);
|
||||
|
||||
// delete old tables, since cannot just change settings
|
||||
|
||||
@ -218,7 +218,7 @@ void AngleTable::settings(int narg, char **arg)
|
||||
|
||||
void AngleTable::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR, "Illegal angle_coeff command");
|
||||
if (narg != 3) error->all(FLERR, "Illegal angle_coeff command: must have 3 arguments");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi;
|
||||
@ -234,7 +234,7 @@ void AngleTable::coeff(int narg, char **arg)
|
||||
|
||||
// error check on table parameters
|
||||
|
||||
if (tb->ninput <= 1) error->one(FLERR, "Invalid angle table length");
|
||||
if (tb->ninput <= 1) error->one(FLERR, "Invalid angle table length: {}", tb->ninput);
|
||||
|
||||
double alo, ahi;
|
||||
alo = tb->afile[0];
|
||||
@ -523,7 +523,7 @@ void AngleTable::param_extract(Table *tb, char *line)
|
||||
} else if (word == "EQ") {
|
||||
tb->theta0 = DEG2RAD * values.next_double();
|
||||
} else {
|
||||
error->one(FLERR, "Invalid keyword in angle table parameters");
|
||||
error->one(FLERR, "Unknown keyword {} in angle table parameters", word);
|
||||
}
|
||||
}
|
||||
} catch (TokenizerException &e) {
|
||||
|
||||
@ -132,7 +132,7 @@ void BondTable::allocate()
|
||||
|
||||
void BondTable::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR, "Illegal bond_style command");
|
||||
if (narg != 2) error->all(FLERR, "Illegal bond_style command: must have 2 arguments");
|
||||
|
||||
tabstyle = NONE;
|
||||
if (strcmp(arg[0], "linear") == 0)
|
||||
@ -140,10 +140,10 @@ void BondTable::settings(int narg, char **arg)
|
||||
else if (strcmp(arg[0], "spline") == 0)
|
||||
tabstyle = SPLINE;
|
||||
else
|
||||
error->all(FLERR, "Unknown table style in bond style table");
|
||||
error->all(FLERR, "Unknown table style {} in bond style table", arg[0]);
|
||||
|
||||
tablength = utils::inumeric(FLERR, arg[1], false, lmp);
|
||||
if (tablength < 2) error->all(FLERR, "Illegal number of bond table entries");
|
||||
if (tablength < 2) error->all(FLERR, "Illegal number of bond table entries: {}", arg[1]);
|
||||
|
||||
// delete old tables, since cannot just change settings
|
||||
|
||||
@ -166,23 +166,21 @@ void BondTable::settings(int narg, char **arg)
|
||||
|
||||
void BondTable::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR, "Illegal bond_coeff command");
|
||||
if (narg != 3) error->all(FLERR, "Illegal bond_coeff command: must have 3 arguments");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
int me;
|
||||
MPI_Comm_rank(world, &me);
|
||||
tables = (Table *) memory->srealloc(tables, (ntables + 1) * sizeof(Table), "bond:tables");
|
||||
Table *tb = &tables[ntables];
|
||||
null_table(tb);
|
||||
if (me == 0) read_table(tb, arg[1], arg[2]);
|
||||
if (comm->me == 0) read_table(tb, arg[1], arg[2]);
|
||||
bcast_table(tb);
|
||||
|
||||
// error check on table parameters
|
||||
|
||||
if (tb->ninput <= 1) error->one(FLERR, "Invalid bond table length");
|
||||
if (tb->ninput <= 1) error->all(FLERR, "Invalid bond table length: {}", tb->ninput);
|
||||
|
||||
tb->lo = tb->rfile[0];
|
||||
tb->hi = tb->rfile[tb->ninput - 1];
|
||||
@ -483,7 +481,7 @@ void BondTable::param_extract(Table *tb, char *line)
|
||||
} else if (word == "EQ") {
|
||||
tb->r0 = values.next_double();
|
||||
} else {
|
||||
error->one(FLERR, "Invalid keyword in bond table parameters");
|
||||
error->one(FLERR, "Unknown keyword {} in bond table parameters", word);
|
||||
}
|
||||
}
|
||||
} catch (TokenizerException &e) {
|
||||
@ -507,9 +505,9 @@ void BondTable::bcast_table(Table *tb)
|
||||
int me;
|
||||
MPI_Comm_rank(world, &me);
|
||||
if (me > 0) {
|
||||
memory->create(tb->rfile, tb->ninput, "angle:rfile");
|
||||
memory->create(tb->efile, tb->ninput, "angle:efile");
|
||||
memory->create(tb->ffile, tb->ninput, "angle:ffile");
|
||||
memory->create(tb->rfile, tb->ninput, "bond:rfile");
|
||||
memory->create(tb->efile, tb->ninput, "bond:efile");
|
||||
memory->create(tb->ffile, tb->ninput, "bond:ffile");
|
||||
}
|
||||
|
||||
MPI_Bcast(tb->rfile, tb->ninput, MPI_DOUBLE, 0, world);
|
||||
|
||||
@ -69,7 +69,6 @@ class BondTable : public Bond {
|
||||
double splint(double *, double *, double *, int, double);
|
||||
|
||||
void uf_lookup(int, double, double &, double &);
|
||||
void u_lookup(int, double, double &);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -697,15 +697,15 @@ void DihedralTable::allocate()
|
||||
|
||||
void DihedralTable::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR,"Illegal dihedral_style command");
|
||||
if (narg != 2) error->all(FLERR,"Illegal dihedral_style command: must have 2 arguments");
|
||||
|
||||
if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR;
|
||||
else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE;
|
||||
else error->all(FLERR,"Unknown table style in dihedral style table");
|
||||
else error->all(FLERR,"Unknown table style {} in dihedral style table", arg[0]);
|
||||
|
||||
tablength = utils::inumeric(FLERR,arg[1],false,lmp);
|
||||
if (tablength < 3)
|
||||
error->all(FLERR,"Illegal number of dihedral table entries");
|
||||
error->all(FLERR,"Illegal number of dihedral table entries: {}", arg[1]);
|
||||
// delete old tables, since cannot just change settings
|
||||
|
||||
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
|
||||
@ -727,7 +727,7 @@ void DihedralTable::settings(int narg, char **arg)
|
||||
|
||||
void DihedralTable::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (narg != 3) error->all(FLERR,"Illegal dihedral_coeff command: must have 3 arguments");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
@ -746,10 +746,9 @@ void DihedralTable::coeff(int narg, char **arg)
|
||||
// --- and resolve issues with periodicity ---
|
||||
|
||||
if (tb->ninput < 2)
|
||||
error->all(FLERR,"Invalid dihedral table length: {}",arg[2]);
|
||||
error->all(FLERR,"Invalid dihedral table length: {}", arg[2]);
|
||||
else if ((tb->ninput == 2) && (tabstyle == SPLINE))
|
||||
error->all(FLERR,"Invalid dihedral spline table length: {} "
|
||||
"(Try linear)",arg[2]);
|
||||
error->all(FLERR,"Invalid dihedral spline table length: {} (Try linear)",arg[2]);
|
||||
|
||||
// check for monotonicity
|
||||
for (int i=0; i < tb->ninput-1; i++) {
|
||||
@ -767,12 +766,10 @@ void DihedralTable::coeff(int narg, char **arg)
|
||||
double phihi = tb->phifile[tb->ninput-1];
|
||||
if (tb->use_degrees) {
|
||||
if ((phihi - philo) >= 360)
|
||||
error->all(FLERR,"Dihedral table angle range must be < 360 "
|
||||
"degrees ({}).",arg[2]);
|
||||
error->all(FLERR,"Dihedral table angle range must be < 360 degrees ({}).",arg[2]);
|
||||
} else {
|
||||
if ((phihi - philo) >= MY_2PI)
|
||||
error->all(FLERR,"Dihedral table angle range must be < 2*PI "
|
||||
"radians ({}).",arg[2]);
|
||||
error->all(FLERR,"Dihedral table angle range must be < 2*PI radians ({}).",arg[2]);
|
||||
}
|
||||
|
||||
// convert phi from degrees to radians
|
||||
@ -1200,7 +1197,7 @@ void DihedralTable::param_extract(Table *tb, char *line)
|
||||
checkU_fname = values.next_string();
|
||||
} else if (word == "CHECKF") {
|
||||
checkF_fname = values.next_string();
|
||||
} else error->one(FLERR,"Invalid keyword in dihedral angle table parameters ({})", word);
|
||||
} else error->one(FLERR,"Unknown keyword {} in dihedral table parameters", word);
|
||||
}
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR, e.what());
|
||||
|
||||
@ -88,12 +88,13 @@ void AtomVecPeri::grow_pointers()
|
||||
|
||||
void AtomVecPeri::create_atom_post(int ilocal)
|
||||
{
|
||||
const auto xinit = atom->x;
|
||||
vfrac[ilocal] = 1.0;
|
||||
rmass[ilocal] = 1.0;
|
||||
s0[ilocal] = DBL_MAX;
|
||||
x0[ilocal][0] = x[ilocal][0];
|
||||
x0[ilocal][1] = x[ilocal][1];
|
||||
x0[ilocal][2] = x[ilocal][2];
|
||||
x0[ilocal][0] = xinit[ilocal][0];
|
||||
x0[ilocal][1] = xinit[ilocal][1];
|
||||
x0[ilocal][2] = xinit[ilocal][2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -103,10 +104,11 @@ void AtomVecPeri::create_atom_post(int ilocal)
|
||||
|
||||
void AtomVecPeri::data_atom_post(int ilocal)
|
||||
{
|
||||
const auto xinit = atom->x;
|
||||
s0[ilocal] = DBL_MAX;
|
||||
x0[ilocal][0] = x[ilocal][0];
|
||||
x0[ilocal][1] = x[ilocal][1];
|
||||
x0[ilocal][2] = x[ilocal][2];
|
||||
x0[ilocal][0] = xinit[ilocal][0];
|
||||
x0[ilocal][1] = xinit[ilocal][1];
|
||||
x0[ilocal][2] = xinit[ilocal][2];
|
||||
|
||||
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid mass in Atoms section of data file");
|
||||
}
|
||||
|
||||
@ -51,6 +51,9 @@ lmpinstalledpkgs.h
|
||||
lmpgitversion.h
|
||||
mliap_model_python_couple.cpp
|
||||
mliap_model_python_couple.h
|
||||
# renamed on 23 February 2023
|
||||
fix_pimd.cpp
|
||||
fix_pimd.h
|
||||
# removed on 20 January 2023
|
||||
atom_vec_mesont.cpp
|
||||
atom_vec_mesont.h
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Package FixPIMD
|
||||
Package FixPIMDNVT
|
||||
Purpose Quantum Path Integral Algorithm for Quantum Chemistry
|
||||
Copyright Voth Group @ University of Chicago
|
||||
Authors Chris Knight & Yuxing Peng (yuxing at uchicago.edu)
|
||||
@ -21,7 +21,7 @@
|
||||
Version 1.0
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_pimd.h"
|
||||
#include "fix_pimd_nvt.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
@ -44,7 +44,7 @@ enum { PIMD, NMPIMD, CMD };
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
FixPIMDNVT::FixPIMDNVT(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
{
|
||||
max_nsend = 0;
|
||||
tag_send = nullptr;
|
||||
@ -85,27 +85,27 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
else if (strcmp(arg[i + 1], "cmd") == 0)
|
||||
method = CMD;
|
||||
else
|
||||
error->universe_all(FLERR, fmt::format("Unknown method parameter {} for fix pimd",
|
||||
arg[i + 1]));
|
||||
error->universe_all(
|
||||
FLERR, fmt::format("Unknown method parameter {} for fix pimd/nvt", arg[i + 1]));
|
||||
} else if (strcmp(arg[i], "fmass") == 0) {
|
||||
fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
|
||||
if ((fmass < 0.0) || (fmass > np))
|
||||
error->universe_all(FLERR, fmt::format("Invalid fmass value {} for fix pimd", fmass));
|
||||
error->universe_all(FLERR, fmt::format("Invalid fmass value {} for fix pimd/nvt", fmass));
|
||||
} else if (strcmp(arg[i], "sp") == 0) {
|
||||
sp = utils::numeric(FLERR, arg[i + 1], false, lmp);
|
||||
if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd");
|
||||
if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd/nvt");
|
||||
} else if (strcmp(arg[i], "temp") == 0) {
|
||||
nhc_temp = utils::numeric(FLERR, arg[i + 1], false, lmp);
|
||||
if (nhc_temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd");
|
||||
if (nhc_temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd/nvt");
|
||||
} else if (strcmp(arg[i], "nhc") == 0) {
|
||||
nhc_nchain = utils::inumeric(FLERR, arg[i + 1], false, lmp);
|
||||
if (nhc_nchain < 2) error->universe_all(FLERR, "Invalid nhc value for fix pimd");
|
||||
if (nhc_nchain < 2) error->universe_all(FLERR, "Invalid nhc value for fix pimd/nvt");
|
||||
} else
|
||||
error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd", arg[i]));
|
||||
error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd/nvt", arg[i]));
|
||||
}
|
||||
|
||||
if (strcmp(update->unit_style, "lj") == 0)
|
||||
error->all(FLERR, "Fix pimd does not support lj units");
|
||||
error->all(FLERR, "Fix pimd/nvt does not support lj units");
|
||||
|
||||
/* Initiation */
|
||||
|
||||
@ -138,7 +138,7 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixPIMD::~FixPIMD()
|
||||
FixPIMDNVT::~FixPIMDNVT()
|
||||
{
|
||||
delete[] mass;
|
||||
atom->delete_callback(id, Atom::GROW);
|
||||
@ -170,7 +170,7 @@ FixPIMD::~FixPIMD()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPIMD::setmask()
|
||||
int FixPIMDNVT::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= POST_FORCE;
|
||||
@ -181,13 +181,13 @@ int FixPIMD::setmask()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::init()
|
||||
void FixPIMDNVT::init()
|
||||
{
|
||||
if (atom->map_style == Atom::MAP_NONE)
|
||||
error->all(FLERR, "Fix pimd requires an atom map, see atom_modify");
|
||||
error->universe_all(FLERR, "Fix pimd/nvt requires an atom map, see atom_modify");
|
||||
|
||||
if (universe->me == 0 && universe->uscreen)
|
||||
fprintf(universe->uscreen, "Fix pimd initializing Path-Integral ...\n");
|
||||
fprintf(universe->uscreen, "Fix pimd/nvt initializing Path-Integral ...\n");
|
||||
|
||||
// prepare the constants
|
||||
|
||||
@ -222,7 +222,7 @@ void FixPIMD::init()
|
||||
fbond = -_fbond * force->mvv2e;
|
||||
|
||||
if (universe->me == 0)
|
||||
printf("Fix pimd -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
|
||||
utils::logmesg(lmp, "Fix pimd/nvt -P/(beta^2 * hbar^2) = {:20.7e} (kcal/mol/A^2)\n\n", fbond);
|
||||
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
@ -241,7 +241,7 @@ void FixPIMD::init()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::setup(int vflag)
|
||||
void FixPIMDNVT::setup(int vflag)
|
||||
{
|
||||
if (universe->me == 0 && universe->uscreen)
|
||||
fprintf(universe->uscreen, "Setting up Path-Integral ...\n");
|
||||
@ -251,7 +251,7 @@ void FixPIMD::setup(int vflag)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::initial_integrate(int /*vflag*/)
|
||||
void FixPIMDNVT::initial_integrate(int /*vflag*/)
|
||||
{
|
||||
nhc_update_v();
|
||||
nhc_update_x();
|
||||
@ -259,14 +259,14 @@ void FixPIMD::initial_integrate(int /*vflag*/)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::final_integrate()
|
||||
void FixPIMDNVT::final_integrate()
|
||||
{
|
||||
nhc_update_v();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::post_force(int /*flag*/)
|
||||
void FixPIMDNVT::post_force(int /*flag*/)
|
||||
{
|
||||
for (int i = 0; i < atom->nlocal; i++)
|
||||
for (int j = 0; j < 3; j++) atom->f[i][j] /= np;
|
||||
@ -293,7 +293,7 @@ void FixPIMD::post_force(int /*flag*/)
|
||||
Nose-Hoover Chains
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::nhc_init()
|
||||
void FixPIMDNVT::nhc_init()
|
||||
{
|
||||
double tau = 1.0 / omega_np;
|
||||
double KT = force->boltz * nhc_temp;
|
||||
@ -309,7 +309,7 @@ void FixPIMD::nhc_init()
|
||||
nhc_eta_dotdot[i][ichain] = 0.0;
|
||||
nhc_eta_mass[i][ichain] = mass0;
|
||||
if ((method == CMD || method == NMPIMD) && universe->iworld == 0)
|
||||
; // do nothing
|
||||
; // do nothing
|
||||
else
|
||||
nhc_eta_mass[i][ichain] *= fmass;
|
||||
}
|
||||
@ -334,7 +334,7 @@ void FixPIMD::nhc_init()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::nhc_update_x()
|
||||
void FixPIMDNVT::nhc_update_x()
|
||||
{
|
||||
int n = atom->nlocal;
|
||||
double **x = atom->x;
|
||||
@ -359,7 +359,7 @@ void FixPIMD::nhc_update_x()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::nhc_update_v()
|
||||
void FixPIMDNVT::nhc_update_v()
|
||||
{
|
||||
int n = atom->nlocal;
|
||||
int *type = atom->type;
|
||||
@ -447,14 +447,14 @@ void FixPIMD::nhc_update_v()
|
||||
Normal Mode PIMD
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::nmpimd_init()
|
||||
void FixPIMDNVT::nmpimd_init()
|
||||
{
|
||||
memory->create(M_x2xp, np, np, "fix_feynman:M_x2xp");
|
||||
memory->create(M_xp2x, np, np, "fix_feynman:M_xp2x");
|
||||
memory->create(M_f2fp, np, np, "fix_feynman:M_f2fp");
|
||||
memory->create(M_fp2f, np, np, "fix_feynman:M_fp2f");
|
||||
|
||||
lam = (double *) memory->smalloc(sizeof(double) * np, "FixPIMD::lam");
|
||||
lam = (double *) memory->smalloc(sizeof(double) * np, "pimd_nvt:lam");
|
||||
|
||||
// Set up eigenvalues
|
||||
|
||||
@ -505,7 +505,7 @@ void FixPIMD::nmpimd_init()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::nmpimd_fill(double **ptr)
|
||||
void FixPIMDNVT::nmpimd_fill(double **ptr)
|
||||
{
|
||||
comm_ptr = ptr;
|
||||
comm->forward_comm(this);
|
||||
@ -513,7 +513,7 @@ void FixPIMD::nmpimd_fill(double **ptr)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::nmpimd_transform(double **src, double **des, double *vector)
|
||||
void FixPIMDNVT::nmpimd_transform(double **src, double **des, double *vector)
|
||||
{
|
||||
int n = atom->nlocal;
|
||||
int m = 0;
|
||||
@ -528,7 +528,7 @@ void FixPIMD::nmpimd_transform(double **src, double **des, double *vector)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::spring_force()
|
||||
void FixPIMDNVT::spring_force()
|
||||
{
|
||||
spring_energy = 0.0;
|
||||
|
||||
@ -576,7 +576,7 @@ void FixPIMD::spring_force()
|
||||
Comm operations
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::comm_init()
|
||||
void FixPIMDNVT::comm_init()
|
||||
{
|
||||
if (size_plan) {
|
||||
delete[] plan_send;
|
||||
@ -634,17 +634,17 @@ void FixPIMD::comm_init()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::comm_exec(double **ptr)
|
||||
void FixPIMDNVT::comm_exec(double **ptr)
|
||||
{
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
if (nlocal > max_nlocal) {
|
||||
max_nlocal = nlocal + 200;
|
||||
int size = sizeof(double) * max_nlocal * 3;
|
||||
buf_recv = (double *) memory->srealloc(buf_recv, size, "FixPIMD:x_recv");
|
||||
buf_recv = (double *) memory->srealloc(buf_recv, size, "FixPIMDNVT:x_recv");
|
||||
|
||||
for (int i = 0; i < np; i++)
|
||||
buf_beads[i] = (double *) memory->srealloc(buf_beads[i], size, "FixPIMD:x_beads[i]");
|
||||
buf_beads[i] = (double *) memory->srealloc(buf_beads[i], size, "FixPIMDNVT:x_beads[i]");
|
||||
}
|
||||
|
||||
// copy local positions
|
||||
@ -666,9 +666,9 @@ void FixPIMD::comm_exec(double **ptr)
|
||||
if (nsend > max_nsend) {
|
||||
max_nsend = nsend + 200;
|
||||
tag_send =
|
||||
(tagint *) memory->srealloc(tag_send, sizeof(tagint) * max_nsend, "FixPIMD:tag_send");
|
||||
buf_send =
|
||||
(double *) memory->srealloc(buf_send, sizeof(double) * max_nsend * 3, "FixPIMD:x_send");
|
||||
(tagint *) memory->srealloc(tag_send, sizeof(tagint) * max_nsend, "FixPIMDNVT:tag_send");
|
||||
buf_send = (double *) memory->srealloc(buf_send, sizeof(double) * max_nsend * 3,
|
||||
"FixPIMDNVT:x_send");
|
||||
}
|
||||
|
||||
// send tags
|
||||
@ -709,7 +709,7 @@ void FixPIMD::comm_exec(double **ptr)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPIMD::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
|
||||
int FixPIMDNVT::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
|
||||
{
|
||||
int i, j, m;
|
||||
|
||||
@ -727,7 +727,7 @@ int FixPIMD::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::unpack_forward_comm(int n, int first, double *buf)
|
||||
void FixPIMDNVT::unpack_forward_comm(int n, int first, double *buf)
|
||||
{
|
||||
int i, m, last;
|
||||
|
||||
@ -744,28 +744,28 @@ void FixPIMD::unpack_forward_comm(int n, int first, double *buf)
|
||||
Memory operations
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixPIMD::memory_usage()
|
||||
double FixPIMDNVT::memory_usage()
|
||||
{
|
||||
return (double) atom->nmax * size_peratom_cols * sizeof(double);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::grow_arrays(int nmax)
|
||||
void FixPIMDNVT::grow_arrays(int nmax)
|
||||
{
|
||||
if (nmax == 0) return;
|
||||
int count = nmax * 3;
|
||||
|
||||
memory->grow(array_atom, nmax, size_peratom_cols, "FixPIMD::array_atom");
|
||||
memory->grow(nhc_eta, count, nhc_nchain, "FixPIMD::nh_eta");
|
||||
memory->grow(nhc_eta_dot, count, nhc_nchain + 1, "FixPIMD::nh_eta_dot");
|
||||
memory->grow(nhc_eta_dotdot, count, nhc_nchain, "FixPIMD::nh_eta_dotdot");
|
||||
memory->grow(nhc_eta_mass, count, nhc_nchain, "FixPIMD::nh_eta_mass");
|
||||
memory->grow(array_atom, nmax, size_peratom_cols, "pimd_nvt:array_atom");
|
||||
memory->grow(nhc_eta, count, nhc_nchain, "pimd_nvt:nh_eta");
|
||||
memory->grow(nhc_eta_dot, count, nhc_nchain + 1, "pimd_nvt:nh_eta_dot");
|
||||
memory->grow(nhc_eta_dotdot, count, nhc_nchain, "pimd_nvt:nh_eta_dotdot");
|
||||
memory->grow(nhc_eta_mass, count, nhc_nchain, "pimd_nvt:nh_eta_mass");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::copy_arrays(int i, int j, int /*delflag*/)
|
||||
void FixPIMDNVT::copy_arrays(int i, int j, int /*delflag*/)
|
||||
{
|
||||
int i_pos = i * 3;
|
||||
int j_pos = j * 3;
|
||||
@ -778,7 +778,7 @@ void FixPIMD::copy_arrays(int i, int j, int /*delflag*/)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPIMD::pack_exchange(int i, double *buf)
|
||||
int FixPIMDNVT::pack_exchange(int i, double *buf)
|
||||
{
|
||||
int offset = 0;
|
||||
int pos = i * 3;
|
||||
@ -797,7 +797,7 @@ int FixPIMD::pack_exchange(int i, double *buf)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPIMD::unpack_exchange(int nlocal, double *buf)
|
||||
int FixPIMDNVT::unpack_exchange(int nlocal, double *buf)
|
||||
{
|
||||
int offset = 0;
|
||||
int pos = nlocal * 3;
|
||||
@ -816,7 +816,7 @@ int FixPIMD::unpack_exchange(int nlocal, double *buf)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPIMD::pack_restart(int i, double *buf)
|
||||
int FixPIMDNVT::pack_restart(int i, double *buf)
|
||||
{
|
||||
int offset = 0;
|
||||
int pos = i * 3;
|
||||
@ -837,7 +837,7 @@ int FixPIMD::pack_restart(int i, double *buf)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPIMD::unpack_restart(int nlocal, int nth)
|
||||
void FixPIMDNVT::unpack_restart(int nlocal, int nth)
|
||||
{
|
||||
double **extra = atom->extra;
|
||||
|
||||
@ -864,21 +864,21 @@ void FixPIMD::unpack_restart(int nlocal, int nth)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPIMD::maxsize_restart()
|
||||
int FixPIMDNVT::maxsize_restart()
|
||||
{
|
||||
return size_peratom_cols + 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPIMD::size_restart(int /*nlocal*/)
|
||||
int FixPIMDNVT::size_restart(int /*nlocal*/)
|
||||
{
|
||||
return size_peratom_cols + 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double FixPIMD::compute_vector(int n)
|
||||
double FixPIMDNVT::compute_vector(int n)
|
||||
{
|
||||
if (n == 0) { return spring_energy; }
|
||||
if (n == 1) { return t_sys; }
|
||||
@ -13,21 +13,22 @@
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
// clang-format off
|
||||
FixStyle(pimd,FixPIMD);
|
||||
FixStyle(pimd,FixPIMDNVT);
|
||||
FixStyle(pimd/nvt,FixPIMDNVT);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef FIX_PIMD_H
|
||||
#define FIX_PIMD_H
|
||||
#ifndef FIX_PIMD_NVT_H
|
||||
#define FIX_PIMD_NVT_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixPIMD : public Fix {
|
||||
class FixPIMDNVT : public Fix {
|
||||
public:
|
||||
FixPIMD(class LAMMPS *, int, char **);
|
||||
~FixPIMD() override;
|
||||
FixPIMDNVT(class LAMMPS *, int, char **);
|
||||
~FixPIMDNVT() override;
|
||||
|
||||
int setmask() override;
|
||||
|
||||
@ -2,18 +2,17 @@ BootStrap: docker
|
||||
From: ubuntu:18.04
|
||||
|
||||
%environment
|
||||
export PATH=/usr/lib/ccache:/usr/local/cuda-11.7/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||
export CUDADIR=/usr/local/cuda-11.7
|
||||
export CUDA_PATH=/usr/local/cuda-11.7
|
||||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.7/lib64:/opt/rocm/lib:/opt/rocm-5.1.3/llvm/lib
|
||||
export LIBRARY_PATH=/usr/local/cuda-11.7/lib64/stubs
|
||||
export PATH=/usr/lib/ccache:/usr/local/cuda-12.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||
export CUDADIR=/usr/local/cuda-12.0
|
||||
export CUDA_PATH=/usr/local/cuda-12.0
|
||||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-12.0/lib64:/opt/rocm/lib:/opt/rocm-5.4.3/llvm/lib
|
||||
export LIBRARY_PATH=/usr/local/cuda-12.0/lib64/stubs
|
||||
%post
|
||||
export DEBIAN_FRONTEND=noninteractive
|
||||
apt-get update
|
||||
apt-get upgrade --no-install-recommends -y
|
||||
|
||||
apt-get install -y --no-install-recommends curl wget libnuma-dev gnupg ca-certificates
|
||||
apt-get install --no-install-recommends -y software-properties-common
|
||||
|
||||
###########################################################################
|
||||
# Latest CMake
|
||||
@ -25,10 +24,10 @@ From: ubuntu:18.04
|
||||
apt install -y cmake
|
||||
|
||||
###########################################################################
|
||||
# ROCm 4.5
|
||||
# ROCm 5.4.3
|
||||
###########################################################################
|
||||
wget https://repo.radeon.com/amdgpu-install/22.10.3/ubuntu/focal/amdgpu-install_22.10.3.50103-1_all.deb
|
||||
apt-get install -y ./amdgpu-install_22.10.3.50103-1_all.deb
|
||||
wget https://repo.radeon.com/amdgpu-install/5.4.3/ubuntu/focal/amdgpu-install_5.4.50403-1_all.deb
|
||||
apt-get install -y ./amdgpu-install_5.4.50403-1_all.deb
|
||||
|
||||
apt-get update
|
||||
apt-get install --no-install-recommends -y \
|
||||
@ -48,6 +47,7 @@ From: ubuntu:18.04
|
||||
###########################################################################
|
||||
# Common Software
|
||||
###########################################################################
|
||||
apt-get install --no-install-recommends -y software-properties-common
|
||||
add-apt-repository ppa:openkim/latest -y
|
||||
apt-get update
|
||||
apt-get install --no-install-recommends -y \
|
||||
@ -120,13 +120,13 @@ From: ubuntu:18.04
|
||||
# CUDA
|
||||
###########################################################################
|
||||
|
||||
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
|
||||
mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
|
||||
apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
|
||||
add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
|
||||
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb
|
||||
dpkg -i cuda-keyring_1.0-1_all.deb
|
||||
rm cuda-keyring_1.0-1_all.deb
|
||||
apt-get update
|
||||
|
||||
export CUDA_PKG_VERSION=11.7
|
||||
export CUDA_PKG_VERSION=12.0
|
||||
export CUDA_DRV_VERSION=525
|
||||
|
||||
apt-get install -y --no-install-recommends \
|
||||
cuda-libraries-${CUDA_PKG_VERSION} \
|
||||
@ -135,7 +135,8 @@ From: ubuntu:18.04
|
||||
cuda-minimal-build-${CUDA_PKG_VERSION} \
|
||||
cuda-compat-$CUDA_PKG_VERSION \
|
||||
libcublas-${CUDA_PKG_VERSION} \
|
||||
libcublas-dev-${CUDA_PKG_VERSION}
|
||||
libcublas-dev-${CUDA_PKG_VERSION} \
|
||||
libnvidia-compute-${CUDA_DRV_VERSION}
|
||||
|
||||
# add missing symlink
|
||||
ln -s /usr/local/cuda-${CUDA_PKG_VERSION}/lib64/stubs/libcuda.so /usr/local/cuda-${CUDA_PKG_VERSION}/lib64/stubs/libcuda.so.1
|
||||
@ -144,8 +145,8 @@ From: ubuntu:18.04
|
||||
# NVIDIA OpenCL
|
||||
###########################################################################
|
||||
|
||||
mkdir -p /etc/OpenCL/vendors
|
||||
echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd
|
||||
test ! -d /etc/OpenCL/vendors && mkdir -p /etc/OpenCL/vendors && \
|
||||
echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd
|
||||
|
||||
|
||||
###########################################################################
|
||||
@ -182,7 +183,7 @@ From: ubuntu:18.04
|
||||
tar -xzf plumed.tar.gz
|
||||
cd plumed-${PLUMED_PKG_VERSION}
|
||||
./configure --disable-doc --prefix=/usr
|
||||
make
|
||||
make -j 4
|
||||
make install
|
||||
cd ../../
|
||||
rm -rvf plumed
|
||||
|
||||
@ -2,11 +2,11 @@ BootStrap: docker
|
||||
From: ubuntu:20.04
|
||||
|
||||
%environment
|
||||
export PATH=/usr/lib/ccache:/usr/local/cuda-11.7/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||
export CUDADIR=/usr/local/cuda-11.7
|
||||
export CUDA_PATH=/usr/local/cuda-11.7
|
||||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.7/lib64:/opt/rocm/lib:/opt/rocm-5.1.3/llvm/lib
|
||||
export LIBRARY_PATH=/usr/local/cuda-11.7/lib64/stubs
|
||||
export PATH=/usr/lib/ccache:/usr/local/cuda-12.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||
export CUDADIR=/usr/local/cuda-12.0
|
||||
export CUDA_PATH=/usr/local/cuda-12.0
|
||||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-12.0/lib64:/opt/rocm/lib:/opt/rocm-5.4.3/llvm/lib
|
||||
export LIBRARY_PATH=/usr/local/cuda-12.0/lib64/stubs
|
||||
%post
|
||||
export DEBIAN_FRONTEND=noninteractive
|
||||
apt-get update
|
||||
@ -15,10 +15,10 @@ From: ubuntu:20.04
|
||||
apt-get install -y --no-install-recommends curl wget libnuma-dev gnupg ca-certificates
|
||||
|
||||
###########################################################################
|
||||
# ROCm 5.1.3
|
||||
# ROCm 5.4.3
|
||||
###########################################################################
|
||||
wget https://repo.radeon.com/amdgpu-install/22.10.3/ubuntu/focal/amdgpu-install_22.10.3.50103-1_all.deb
|
||||
apt-get install -y ./amdgpu-install_22.10.3.50103-1_all.deb
|
||||
wget https://repo.radeon.com/amdgpu-install/5.4.3/ubuntu/focal/amdgpu-install_5.4.50403-1_all.deb
|
||||
apt-get install -y ./amdgpu-install_5.4.50403-1_all.deb
|
||||
|
||||
apt-get update
|
||||
apt-get install --no-install-recommends -y \
|
||||
@ -107,13 +107,13 @@ From: ubuntu:20.04
|
||||
# CUDA
|
||||
###########################################################################
|
||||
|
||||
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
|
||||
mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
|
||||
apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/3bf863cc.pub
|
||||
add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
|
||||
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
|
||||
dpkg -i cuda-keyring_1.0-1_all.deb
|
||||
rm cuda-keyring_1.0-1_all.deb
|
||||
apt-get update
|
||||
|
||||
export CUDA_PKG_VERSION=11.5
|
||||
export CUDA_PKG_VERSION=12.0
|
||||
export CUDA_DRV_VERSION=525
|
||||
|
||||
apt-get install -y --no-install-recommends \
|
||||
cuda-libraries-${CUDA_PKG_VERSION} \
|
||||
@ -122,7 +122,8 @@ From: ubuntu:20.04
|
||||
cuda-minimal-build-${CUDA_PKG_VERSION} \
|
||||
cuda-compat-$CUDA_PKG_VERSION \
|
||||
libcublas-${CUDA_PKG_VERSION} \
|
||||
libcublas-dev-${CUDA_PKG_VERSION}
|
||||
libcublas-dev-${CUDA_PKG_VERSION} \
|
||||
libnvidia-compute-${CUDA_DRV_VERSION}
|
||||
|
||||
# add missing symlink
|
||||
ln -s /usr/local/cuda-${CUDA_PKG_VERSION}/lib64/stubs/libcuda.so /usr/local/cuda-${CUDA_PKG_VERSION}/lib64/stubs/libcuda.so.1
|
||||
@ -131,9 +132,8 @@ From: ubuntu:20.04
|
||||
# NVIDIA OpenCL
|
||||
###########################################################################
|
||||
|
||||
mkdir -p /etc/OpenCL/vendors
|
||||
echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd
|
||||
|
||||
test ! -d /etc/OpenCL/vendors && mkdir -p /etc/OpenCL/vendors && \
|
||||
echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd
|
||||
|
||||
###########################################################################
|
||||
# KIM-API
|
||||
@ -169,7 +169,7 @@ From: ubuntu:20.04
|
||||
tar -xzf plumed.tar.gz
|
||||
cd plumed-${PLUMED_PKG_VERSION}
|
||||
./configure --disable-doc --prefix=/usr
|
||||
make
|
||||
make -j 4
|
||||
make install
|
||||
cd ../../
|
||||
rm -rvf plumed
|
||||
|
||||
Reference in New Issue
Block a user