From 9031c230801cc60fca3445134224337880466fca Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 16 Apr 2021 14:14:18 +0200 Subject: [PATCH 01/12] add extended dpd (dpdext & dpdext_tstat) --- doc/src/pair_dpdext.rst | 137 + examples/USER/dpdext/README | 10 + examples/USER/dpdext/dpdext/dpdext.data | 2196 +++++++++++++++++ examples/USER/dpdext/dpdext/in.dpdext | 44 + .../dpdext/dpdext/log.10Mar21.dpdext.g++.1 | 201 ++ .../dpdext/dpdext/log.10Mar21.dpdext.g++.4 | 201 ++ .../USER/dpdext/dpdext_tstat/cg_spce.data | 2196 +++++++++++++++++ .../dpdext/dpdext_tstat/cg_spce_table.pot | 354 +++ examples/USER/dpdext/dpdext_tstat/in.cg_spce | 31 + .../dpdext_tstat/log.10Mar21.dpdext.g++.1 | 293 +++ .../dpdext_tstat/log.10Mar21.dpdext.g++.4 | 293 +++ src/Makefile | 2 +- src/USER-DPDEXT/README | 10 + src/USER-DPDEXT/pair_dpd_ext.cpp | 496 ++++ src/USER-DPDEXT/pair_dpd_ext.h | 86 + src/USER-DPDEXT/pair_dpd_tstat_ext.cpp | 376 +++ src/USER-DPDEXT/pair_dpd_tstat_ext.h | 62 + 17 files changed, 6987 insertions(+), 1 deletion(-) create mode 100644 doc/src/pair_dpdext.rst create mode 100644 examples/USER/dpdext/README create mode 100755 examples/USER/dpdext/dpdext/dpdext.data create mode 100755 examples/USER/dpdext/dpdext/in.dpdext create mode 100644 examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 create mode 100644 examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 create mode 100755 examples/USER/dpdext/dpdext_tstat/cg_spce.data create mode 100755 examples/USER/dpdext/dpdext_tstat/cg_spce_table.pot create mode 100755 examples/USER/dpdext/dpdext_tstat/in.cg_spce create mode 100644 examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 create mode 100644 examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 create mode 100644 src/USER-DPDEXT/README create mode 100644 src/USER-DPDEXT/pair_dpd_ext.cpp create mode 100644 src/USER-DPDEXT/pair_dpd_ext.h create mode 100644 src/USER-DPDEXT/pair_dpd_tstat_ext.cpp create mode 100644 src/USER-DPDEXT/pair_dpd_tstat_ext.h diff --git a/doc/src/pair_dpdext.rst b/doc/src/pair_dpdext.rst new file mode 100644 index 0000000000..301f9f3ea0 --- /dev/null +++ b/doc/src/pair_dpdext.rst @@ -0,0 +1,137 @@ +.. index:: pair_style dpdext + +pair_style dpdext command +========================== + +pair_style dpdext/tstat command +================================ + +Syntax +"""""" + + +.. code-block:: LAMMPS + + pair_style dpdext T cutoff seed + pair_style dpdext/tstat Tstart Tstop cutoff seed + +* T = temperature (temperature units) +* Tstart,Tstop = desired temperature at start/end of run (temperature units) +* cutoff = global cutoff for DPD interactions (distance units) +* seed = random # seed (positive integer) + +Examples +"""""""" + + +.. code-block:: LAMMPS + + pair_style dpdext 1.0 2.5 34387 + pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2 + pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2 + + pair_style dpdext/tstat 1.0 1.0 2.5 34387 + pair_coeff 1 1 4.5 4.5 0.5 0.5 1.2 + pair_coeff 1 2 4.5 4.5 0.5 0.5 1.2 + +Description +""""""""""" + +The style *dpdext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. + +Style *dpdext/tstat* invokes an extended DPD thermostat on pairwise interactions, which is equivalent to the non-conservative portion of the extended DPD force field. To use *dpdext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. + +For the style *dpdext*\ , the force on atom I due to atom J is given as a sum +of 3 terms + +.. math:: + + \mathbf{f} = & f^C + f^D + f^R \qquad \qquad r < r_c \\ + f^C = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\ + f^D = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij} - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\ + f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ + w(r) = & 1 - r/r_c \\ + +where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\a` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. + +For the style *dpdext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. + +For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. + +For the style *dpdext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. + +For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. + +For the style *dpdext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: + +* A (force units) +* :math:`\gamma_{\perp}` (force/velocity units) +* :math:`\gamma_{\parallel}` (force/velocity units) +* :math:`s_{\perp}` (unitless) +* :math:`s_{\parallel}` (unitless) +* :math:`r_c` (distance units) + +The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. + + +For the style *dpdext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. + +.. note:: + + If you are modeling DPD polymer chains, you may want to use the :doc:`pair_style srp ` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. + +.. note:: + + The virial calculation for pressure when using this pair style includes all the components of force listed above, including the random force. + +---------- + + +**Mixing, shift, table, tail correction, restart, rRESPA info**\ : + +The style *dpdext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. + +The pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`. + +The :doc:`pair_modify ` table option is not relevant for the style *dpdext*. + +The style *dpdext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. + +The pair styles can only be used via the pair keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords. + +The style *dpdext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. + +---------- + + +Restrictions +"""""""""""" + +The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpdext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. + +The pair styles require to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. + +The pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the :doc:`read_restart ` command for more details. + +Related commands +"""""""""""""""" + +:doc:`pair_style dpd `, :doc:`pair_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair_style srp ` + +**Default:** none + + +---------- + + +.. _Groot: + + + +**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). + +.. _Junghans: + + + +**(Junghans)** Junghans, Praprotnik and Kremer, Soft Matter 4, 156, 1119-1128 (2008). diff --git a/examples/USER/dpdext/README b/examples/USER/dpdext/README new file mode 100644 index 0000000000..43d66c4bd3 --- /dev/null +++ b/examples/USER/dpdext/README @@ -0,0 +1,10 @@ +Examples for Extended Dissipative Particle Dynamics (DPD) +--------------------------------------------------------- +This directory contains examples for extended DPD simulations + +1) 'dpdext' - test case (DPD fluid) for 'dpdext' pair style (in.dpdext) and an initial + configuration (dpdext.data) + +2) 'dpdext_tstat' - test case (coarse-grained SPC/E water) for 'dpdext/tstat' pair style + (in.cg_spce), an initial configuration (dpdext.data) and tabulated potential + (cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water. diff --git a/examples/USER/dpdext/dpdext/dpdext.data b/examples/USER/dpdext/dpdext/dpdext.data new file mode 100755 index 0000000000..dddbf6ad6c --- /dev/null +++ b/examples/USER/dpdext/dpdext/dpdext.data @@ -0,0 +1,2196 @@ + DPD Fluid + + 2180 atoms + + 1 atom types + + 0.0000000E+00 40.310000000000 xlo xhi + 0.0000000E+00 40.310000000000 ylo yhi + 0.0000000E+00 40.310000000000 zlo zhi + + Masses + +1 18.01540 + + Atoms + +1 1 2.815000E+01 5.430000E+00 2.370000E+00 +2 1 1.890000E+00 2.957000E+01 1.761000E+01 +3 1 8.920000E+00 3.556000E+01 8.240000E+00 +4 1 2.307000E+01 9.600000E+00 4.710000E+00 +5 1 1.688000E+01 8.940000E+00 3.880000E+00 +6 1 2.571000E+01 1.277000E+01 1.056000E+01 +7 1 2.788000E+01 3.328000E+01 1.300000E-01 +8 1 3.287000E+01 2.050000E+00 1.368000E+01 +9 1 4.900000E+00 2.183000E+01 1.751000E+01 +10 1 9.670000E+00 3.108000E+01 1.843000E+01 +11 1 1.233000E+01 3.490000E+00 1.091000E+01 +12 1 6.630000E+00 1.581000E+01 3.455000E+01 +13 1 3.951000E+01 2.047000E+01 2.288000E+01 +14 1 3.977000E+01 3.173000E+01 9.060000E+00 +15 1 5.370000E+00 8.940000E+00 3.646000E+01 +16 1 2.129000E+01 3.853000E+01 3.468000E+01 +17 1 1.987000E+01 2.677000E+01 3.762000E+01 +18 1 2.658000E+01 3.167000E+01 2.280000E+00 +19 1 1.231000E+01 3.336000E+01 1.098000E+01 +20 1 7.310000E+00 1.410000E+01 1.654000E+01 +21 1 3.388000E+01 2.584000E+01 1.677000E+01 +22 1 1.115000E+01 3.070000E+00 3.992000E+01 +23 1 3.171000E+01 3.195000E+01 2.267000E+01 +24 1 5.960000E+00 3.507000E+01 1.230000E+01 +25 1 2.904000E+01 1.740000E+00 9.460000E+00 +26 1 1.539000E+01 2.686000E+01 2.030000E+00 +27 1 3.890000E+00 2.148000E+01 2.877000E+01 +28 1 4.550000E+00 2.800000E+01 2.431000E+01 +29 1 9.680000E+00 3.992000E+01 2.964000E+01 +30 1 2.560000E+00 3.939000E+01 2.987000E+01 +31 1 4.960000E+00 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7.780000E+00 1.678000E+01 +2134 1 3.330000E+01 3.916000E+01 1.899000E+01 +2135 1 3.264000E+01 4.210000E+00 2.427000E+01 +2136 1 1.114000E+01 8.100000E+00 2.329000E+01 +2137 1 1.026000E+01 8.900000E-01 2.724000E+01 +2138 1 2.257000E+01 2.754000E+01 3.789000E+01 +2139 1 2.495000E+01 2.840000E+01 3.687000E+01 +2140 1 3.977000E+01 2.981000E+01 5.800000E+00 +2141 1 2.256000E+01 3.840000E+00 6.270000E+00 +2142 1 7.580000E+00 1.410000E+01 3.520000E+00 +2143 1 1.702000E+01 3.918000E+01 9.200000E+00 +2144 1 2.898000E+01 1.973000E+01 3.924000E+01 +2145 1 4.020000E+01 1.529000E+01 2.723000E+01 +2146 1 7.220000E+00 2.652000E+01 2.819000E+01 +2147 1 1.020000E+01 4.510000E+00 2.913000E+01 +2148 1 1.075000E+01 1.786000E+01 8.600000E+00 +2149 1 2.851000E+01 6.170000E+00 2.682000E+01 +2150 1 1.450000E+00 2.132000E+01 4.020000E+00 +2151 1 4.360000E+00 1.142000E+01 4.500000E-01 +2152 1 6.800000E+00 2.136000E+01 2.166000E+01 +2153 1 1.803000E+01 3.907000E+01 4.900000E+00 +2154 1 3.187000E+01 1.368000E+01 1.983000E+01 +2155 1 3.040000E+01 9.820000E+00 3.786000E+01 +2156 1 3.694000E+01 5.550000E+00 1.614000E+01 +2157 1 1.520000E+00 2.840000E+00 7.180000E+00 +2158 1 7.550000E+00 3.788000E+01 1.150000E+00 +2159 1 3.262000E+01 8.680000E+00 1.004000E+01 +2160 1 9.400000E+00 1.616000E+01 1.029000E+01 +2161 1 5.980000E+00 1.628000E+01 2.001000E+01 +2162 1 1.590000E+00 2.898000E+01 2.510000E+00 +2163 1 2.260000E+00 2.503000E+01 2.702000E+01 +2164 1 3.725000E+01 2.886000E+01 1.681000E+01 +2165 1 1.751000E+01 3.490000E+01 2.327000E+01 +2166 1 2.729000E+01 1.952000E+01 2.661000E+01 +2167 1 8.190000E+00 3.201000E+01 2.417000E+01 +2168 1 7.080000E+00 2.577000E+01 1.091000E+01 +2169 1 3.065000E+01 6.030000E+00 2.910000E+00 +2170 1 2.078000E+01 1.994000E+01 1.970000E+01 +2171 1 7.100000E-01 7.250000E+00 1.784000E+01 +2172 1 3.287000E+01 8.740000E+00 1.891000E+01 +2173 1 1.178000E+01 2.800000E+01 1.470000E+01 +2174 1 2.178000E+01 2.015000E+01 3.462000E+01 +2175 1 3.874000E+01 1.992000E+01 1.613000E+01 +2176 1 3.554000E+01 3.239000E+01 3.856000E+01 +2177 1 1.772000E+01 4.020000E+01 1.210000E+00 +2178 1 2.093000E+01 1.558000E+01 2.323000E+01 +2179 1 8.900000E+00 2.592000E+01 3.849000E+01 +2180 1 1.428000E+01 6.460000E+00 3.351000E+01 diff --git a/examples/USER/dpdext/dpdext/in.dpdext b/examples/USER/dpdext/dpdext/in.dpdext new file mode 100755 index 0000000000..3101be9a1c --- /dev/null +++ b/examples/USER/dpdext/dpdext/in.dpdext @@ -0,0 +1,44 @@ +# DPD Fluid + +variable T equal 1.0 +variable rc equal 1.0 +variable rcD equal 1.2 + +units lj +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +### create box and configuration +variable L equal 5.0 +lattice fcc 3.0 +region simBox block 0 ${L} 0 ${L} 0 ${L} +create_box 2 simBox +#create_atoms 1 region simBox +create_atoms 1 random 100 132456 simBox +create_atoms 2 random 100 132456 simBox +mass 1 1.0 +mass 2 2.0 +### + +pair_style dpdext ${T} ${rc} 3854262 + +pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} +pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} +pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD} + +timestep 0.01 +run_style verlet + +velocity all create ${T} 68768932 + +thermo_style custom step time temp press +thermo 500 + +fix 1 all nve + +run 50000 + +write_data final.data pair ij \ No newline at end of file diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 b/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 new file mode 100644 index 0000000000..ef61ed11b8 --- /dev/null +++ b/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 @@ -0,0 +1,201 @@ +LAMMPS (10 Mar 2021) +# DPD Fluid + +variable T equal 1.0 +variable rc equal 1.0 +variable rcD equal 1.2 + +units lj +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +### create box and configuration +variable L equal 5.0 +lattice fcc 3.0 +Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424 +region simBox block 0 ${L} 0 ${L} 0 ${L} +region simBox block 0 5 0 ${L} 0 ${L} +region simBox block 0 5 0 5 0 ${L} +region simBox block 0 5 0 5 0 5 +create_box 2 simBox +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.5032121 5.5032121 5.5032121) + 1 by 1 by 1 MPI processor grid +#create_atoms 1 region simBox +create_atoms 1 random 100 132456 simBox +Created 100 atoms + create_atoms CPU = 0.001 seconds +create_atoms 2 random 100 132456 simBox +Created 100 atoms + create_atoms CPU = 0.000 seconds +mass 1 1.0 +mass 2 2.0 +### + +pair_style dpdext ${T} ${rc} 3854262 +pair_style dpdext 1 ${rc} 3854262 +pair_style dpdext 1 1 3854262 + +pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} +pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} +pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD} + +timestep 0.01 +run_style verlet + +velocity all create ${T} 68768932 +velocity all create 1 68768932 + +thermo_style custom step time temp press +thermo 500 + +fix 1 all nve + +run 50000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.52 + ghost atom cutoff = 1.52 + binsize = 0.76, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair dpdext, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.087 | 3.087 | 3.087 Mbytes +Step Time Temp Press + 0 0 1 8.8992215 + 500 5 0.93699892 8.1219621 + 1000 10 0.99211009 7.4709658 + 1500 15 0.91190984 8.828742 + 2000 20 0.90749036 9.1258378 + 2500 25 0.97960404 7.085574 + 3000 30 1.0314836 6.8400202 + 3500 35 1.0137019 7.2346862 + 4000 40 0.98189616 6.7265624 + 4500 45 1.0127497 6.6718402 + 5000 50 0.90659787 7.4911309 + 5500 55 1.0257891 6.8163777 + 6000 60 1.0596209 7.8511522 + 6500 65 0.95679865 8.4091947 + 7000 70 1.012617 7.4162991 + 7500 75 1.0990412 7.160905 + 8000 80 0.91085269 7.6861008 + 8500 85 1.1000209 6.4818934 + 9000 90 0.99982282 8.1312206 + 9500 95 1.1330979 7.7167159 + 10000 100 0.98147521 8.4394218 + 10500 105 1.0254021 7.23574 + 11000 110 0.94064194 7.9766833 + 11500 115 1.012364 8.4285752 + 12000 120 0.94787277 7.0819132 + 12500 125 1.13729 7.9636837 + 13000 130 1.1200519 7.1570016 + 13500 135 0.96797085 8.9794827 + 14000 140 1.0271217 7.4193307 + 14500 145 1.0154843 7.3495938 + 15000 150 1.0408558 7.3047404 + 15500 155 1.0801685 6.8072764 + 16000 160 0.9921089 7.3200563 + 16500 165 0.92952943 7.281934 + 17000 170 0.87149276 7.6508951 + 17500 175 0.92808338 6.4774803 + 18000 180 1.008898 7.1954708 + 18500 185 0.95962238 8.0257166 + 19000 190 0.99501354 8.5364854 + 19500 195 0.97420657 8.3140832 + 20000 200 0.99926953 7.7840117 + 20500 205 1.0503096 7.9214552 + 21000 210 0.97782558 7.4084605 + 21500 215 0.90363877 7.2867997 + 22000 220 1.0045369 7.7341956 + 22500 225 1.0319487 8.4140146 + 23000 230 1.006863 7.6023442 + 23500 235 0.90302749 8.0230562 + 24000 240 1.0768463 7.7315652 + 24500 245 1.0529241 7.9835388 + 25000 250 0.96057288 6.9591339 + 25500 255 0.98941425 7.4287206 + 26000 260 0.99120107 7.0440907 + 26500 265 0.94017831 7.9499345 + 27000 270 0.93766339 8.118634 + 27500 275 0.98309918 7.9865412 + 28000 280 1.0191736 8.3330592 + 28500 285 0.99546328 8.3419405 + 29000 290 0.95703084 7.313665 + 29500 295 1.0122694 8.1900103 + 30000 300 1.0758207 8.2876755 + 30500 305 1.0981472 6.4742286 + 31000 310 1.0356215 6.4857599 + 31500 315 0.95584989 8.4446078 + 32000 320 1.0591455 8.3936647 + 32500 325 0.92674627 7.0391747 + 33000 330 0.93486399 7.6892746 + 33500 335 1.0772579 7.1395468 + 34000 340 1.1029975 7.4249835 + 34500 345 0.9845352 6.3478805 + 35000 350 1.1004884 8.0179815 + 35500 355 0.97596833 8.1652441 + 36000 360 1.0026086 7.8100907 + 36500 365 1.0242946 7.4683685 + 37000 370 0.98485255 7.9021959 + 37500 375 1.078371 8.726722 + 38000 380 0.99139516 7.3585787 + 38500 385 1.0531594 8.5221732 + 39000 390 1.0290073 7.0905003 + 39500 395 1.0368491 8.0293456 + 40000 400 1.0520724 7.6372283 + 40500 405 0.94925657 8.9578914 + 41000 410 0.99919726 7.7207005 + 41500 415 1.0507736 6.9924906 + 42000 420 1.0442899 7.8115665 + 42500 425 1.0192672 8.5123404 + 43000 430 0.9784861 8.0556966 + 43500 435 0.99592222 8.0665153 + 44000 440 0.95621235 8.4132911 + 44500 445 0.93400296 7.3266133 + 45000 450 1.0389454 7.2458003 + 45500 455 1.1076673 6.5868539 + 46000 460 1.0826918 7.9286381 + 46500 465 0.93589963 8.5310745 + 47000 470 1.0352143 6.6366463 + 47500 475 1.0497186 8.5074329 + 48000 480 0.96107226 7.7505527 + 48500 485 1.1061337 8.2753596 + 49000 490 1.0337198 7.5777833 + 49500 495 0.94052507 7.3661443 + 50000 500 0.98527818 7.1746325 +Loop time of 10.2559 on 1 procs for 50000 steps with 200 atoms + +Performance: 4212216.548 tau/day, 4875.251 timesteps/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.9888 | 8.9888 | 8.9888 | 0.0 | 87.65 +Neigh | 0.832 | 0.832 | 0.832 | 0.0 | 8.11 +Comm | 0.30913 | 0.30913 | 0.30913 | 0.0 | 3.01 +Output | 0.0021966 | 0.0021966 | 0.0021966 | 0.0 | 0.02 +Modify | 0.084161 | 0.084161 | 0.084161 | 0.0 | 0.82 +Other | | 0.03957 | | | 0.39 + +Nlocal: 200.000 ave 200 max 200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 547.000 ave 547 max 547 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1651.00 ave 1651 max 1651 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1651 +Ave neighs/atom = 8.2550000 +Neighbor list builds = 5000 +Dangerous builds = 5000 + +write_data final.data pair ij +System init for write_data ... +Total wall time: 0:00:10 diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 b/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 new file mode 100644 index 0000000000..bbbf47a46c --- /dev/null +++ b/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 @@ -0,0 +1,201 @@ +LAMMPS (10 Mar 2021) +# DPD Fluid + +variable T equal 1.0 +variable rc equal 1.0 +variable rcD equal 1.2 + +units lj +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +### create box and configuration +variable L equal 5.0 +lattice fcc 3.0 +Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424 +region simBox block 0 ${L} 0 ${L} 0 ${L} +region simBox block 0 5 0 ${L} 0 ${L} +region simBox block 0 5 0 5 0 ${L} +region simBox block 0 5 0 5 0 5 +create_box 2 simBox +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.5032121 5.5032121 5.5032121) + 1 by 2 by 2 MPI processor grid +#create_atoms 1 region simBox +create_atoms 1 random 100 132456 simBox +Created 100 atoms + create_atoms CPU = 0.001 seconds +create_atoms 2 random 100 132456 simBox +Created 100 atoms + create_atoms CPU = 0.000 seconds +mass 1 1.0 +mass 2 2.0 +### + +pair_style dpdext ${T} ${rc} 3854262 +pair_style dpdext 1 ${rc} 3854262 +pair_style dpdext 1 1 3854262 + +pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} +pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} +pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD} + +timestep 0.01 +run_style verlet + +velocity all create ${T} 68768932 +velocity all create 1 68768932 + +thermo_style custom step time temp press +thermo 500 + +fix 1 all nve + +run 50000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.52 + ghost atom cutoff = 1.52 + binsize = 0.76, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair dpdext, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.064 | 3.064 | 3.064 Mbytes +Step Time Temp Press + 0 0 1 7.9021356 + 500 5 0.937908 7.0735774 + 1000 10 0.89467862 7.7074585 + 1500 15 1.0197239 8.6662041 + 2000 20 1.0306203 8.0831978 + 2500 25 0.94106312 7.4609953 + 3000 30 1.0217162 7.7000536 + 3500 35 0.9694633 6.9496101 + 4000 40 0.89886564 7.5844291 + 4500 45 0.9914389 6.5459858 + 5000 50 1.0503316 7.1639528 + 5500 55 0.95397384 7.2900451 + 6000 60 0.91097079 7.4484481 + 6500 65 1.0212125 8.6396803 + 7000 70 0.84788375 9.2247619 + 7500 75 1.0477577 7.9631111 + 8000 80 1.0473514 7.2904431 + 8500 85 1.0482936 7.9668363 + 9000 90 1.0239558 7.1715815 + 9500 95 1.0727305 8.2075133 + 10000 100 0.96755536 7.8062307 + 10500 105 1.0357222 8.2249507 + 11000 110 1.053488 6.8283393 + 11500 115 0.89283913 8.9044509 + 12000 120 1.0085932 8.1844316 + 12500 125 0.84259725 6.9608932 + 13000 130 1.0559908 7.5907714 + 13500 135 0.95175487 8.8486631 + 14000 140 0.954129 8.2199072 + 14500 145 1.0034836 8.6956618 + 15000 150 0.99411864 7.3723436 + 15500 155 1.0876662 8.5906664 + 16000 160 0.98613154 7.6599681 + 16500 165 1.0355659 6.7243908 + 17000 170 1.0838802 7.5905171 + 17500 175 0.95966717 7.3268842 + 18000 180 0.91267962 8.1126836 + 18500 185 0.9625394 8.0889468 + 19000 190 1.0209688 7.2104928 + 19500 195 0.93315956 8.3484128 + 20000 200 1.0430989 6.4154856 + 20500 205 1.037892 7.3727084 + 21000 210 1.0551654 8.3732908 + 21500 215 0.97922101 8.0403654 + 22000 220 1.0480356 9.2304431 + 22500 225 1.0009668 8.0807868 + 23000 230 1.0808549 7.9128664 + 23500 235 0.99282487 7.550466 + 24000 240 0.96893196 8.0123396 + 24500 245 0.96945612 6.9129899 + 25000 250 0.9373397 6.2942852 + 25500 255 0.98958822 7.8259805 + 26000 260 0.97971277 7.3263113 + 26500 265 0.91588062 8.284996 + 27000 270 1.0045677 7.490418 + 27500 275 0.92664827 7.2434156 + 28000 280 0.98527367 7.1695053 + 28500 285 0.97862372 8.2272887 + 29000 290 1.067876 8.3157621 + 29500 295 1.0688998 7.5106281 + 30000 300 1.117583 8.8135518 + 30500 305 1.035452 7.3572033 + 31000 310 1.03275 8.1486503 + 31500 315 0.96000074 7.6740792 + 32000 320 0.91763282 7.6603754 + 32500 325 0.99394287 8.8127132 + 33000 330 1.0021499 7.9881263 + 33500 335 0.97639399 8.2361021 + 34000 340 1.0309313 8.2918535 + 34500 345 1.0214124 7.3886765 + 35000 350 1.0029326 8.2745874 + 35500 355 1.0634485 6.4161924 + 36000 360 1.0242523 7.4099968 + 36500 365 1.0302234 8.0604043 + 37000 370 1.0143945 7.34914 + 37500 375 0.99553421 6.8818266 + 38000 380 1.0073546 7.6254332 + 38500 385 1.0068118 7.4673312 + 39000 390 0.95181135 6.1644033 + 39500 395 0.98964849 8.501371 + 40000 400 0.99441011 8.1515808 + 40500 405 1.0339683 7.6747037 + 41000 410 0.99467835 7.8743708 + 41500 415 1.0231331 7.3169584 + 42000 420 0.94617359 8.0079888 + 42500 425 1.0163237 7.7949198 + 43000 430 0.97039825 8.8842702 + 43500 435 1.0326956 7.6700965 + 44000 440 1.1106283 8.2900664 + 44500 445 0.96697428 7.0408563 + 45000 450 1.0137186 6.8316108 + 45500 455 1.0531692 8.0051631 + 46000 460 1.0382619 7.2937333 + 46500 465 0.90277459 7.9676952 + 47000 470 1.00751 8.7594948 + 47500 475 0.95565907 8.320444 + 48000 480 1.0396091 7.9262425 + 48500 485 1.0349892 8.333501 + 49000 490 0.9759139 7.4839858 + 49500 495 0.91538068 7.1780491 + 50000 500 1.0310634 7.1522794 +Loop time of 9.14414 on 4 procs for 50000 steps with 200 atoms + +Performance: 4724338.550 tau/day, 5467.984 timesteps/s +96.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.0824 | 5.212 | 5.3376 | 5.1 | 57.00 +Neigh | 0.49498 | 0.50029 | 0.505 | 0.6 | 5.47 +Comm | 3.1637 | 3.2822 | 3.4143 | 6.3 | 35.89 +Output | 0.0025831 | 0.003088 | 0.004569 | 1.5 | 0.03 +Modify | 0.067261 | 0.068927 | 0.070535 | 0.5 | 0.75 +Other | | 0.07762 | | | 0.85 + +Nlocal: 50.0000 ave 53 max 46 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 296.000 ave 301 max 290 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 410.750 ave 431 max 357 min +Histogram: 1 0 0 0 0 0 0 0 0 3 + +Total # of neighbors = 1643 +Ave neighs/atom = 8.2150000 +Neighbor list builds = 5000 +Dangerous builds = 5000 + +write_data final.data pair ij +System init for write_data ... +Total wall time: 0:00:09 diff --git a/examples/USER/dpdext/dpdext_tstat/cg_spce.data b/examples/USER/dpdext/dpdext_tstat/cg_spce.data new file mode 100755 index 0000000000..d487e2c73c --- /dev/null +++ b/examples/USER/dpdext/dpdext_tstat/cg_spce.data @@ -0,0 +1,2196 @@ + Coarse-Grained SPC/E Water + + 2180 atoms + + 1 atom types + + 0.0000000E+00 40.310000000000 xlo xhi + 0.0000000E+00 40.310000000000 ylo yhi + 0.0000000E+00 40.310000000000 zlo zhi + + Masses + +1 18.01540 + + Atoms + +1 1 2.815000E+01 5.430000E+00 2.370000E+00 +2 1 1.890000E+00 2.957000E+01 1.761000E+01 +3 1 8.920000E+00 3.556000E+01 8.240000E+00 +4 1 2.307000E+01 9.600000E+00 4.710000E+00 +5 1 1.688000E+01 8.940000E+00 3.880000E+00 +6 1 2.571000E+01 1.277000E+01 1.056000E+01 +7 1 2.788000E+01 3.328000E+01 1.300000E-01 +8 1 3.287000E+01 2.050000E+00 1.368000E+01 +9 1 4.900000E+00 2.183000E+01 1.751000E+01 +10 1 9.670000E+00 3.108000E+01 1.843000E+01 +11 1 1.233000E+01 3.490000E+00 1.091000E+01 +12 1 6.630000E+00 1.581000E+01 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8.480000E+00 -1.994691E-03 -1.425700E-03 +326 8.500000E+00 -1.945329E-03 -3.708091E-03 +327 8.520000E+00 -1.867098E-03 -4.115259E-03 +328 8.540000E+00 -1.780711E-03 -4.523663E-03 +329 8.560000E+00 -1.686143E-03 -4.933304E-03 +330 8.580000E+00 -1.583370E-03 -5.344181E-03 +331 8.600000E+00 -1.472368E-03 -5.756296E-03 +332 8.620000E+00 -1.328792E-03 -8.394009E-03 +333 8.640000E+00 -1.144899E-03 -9.787974E-03 +334 8.660000E+00 -9.455644E-04 -9.938189E-03 +335 8.680000E+00 -7.556630E-04 -8.844656E-03 +336 8.700000E+00 -6.000698E-04 -6.507373E-03 +337 8.720000E+00 -5.364035E-04 -3.286769E-04 +338 8.740000E+00 -5.681458E-04 3.033482E-03 +339 8.760000E+00 -6.389659E-04 3.579102E-03 +340 8.780000E+00 -6.925330E-04 1.308185E-03 +341 8.800000E+00 -6.725164E-04 -3.779270E-03 +342 8.820000E+00 -5.113768E-04 -1.169180E-02 +343 8.840000E+00 -2.305599E-04 -1.574700E-02 +344 8.860000E+00 9.278768E-05 -1.594487E-02 +345 8.880000E+00 3.815195E-04 -1.228542E-02 +346 8.900000E+00 5.584889E-04 -4.768636E-03 +347 8.920000E+00 6.079481E-04 -2.335309E-04 +348 8.940000E+00 5.700798E-04 3.964121E-03 +349 8.960000E+00 4.516330E-04 7.824320E-03 +350 8.980000E+00 2.593567E-04 1.134707E-02 +351 9.000000E+00 0.000000E+00 1.453236E-02 diff --git a/examples/USER/dpdext/dpdext_tstat/in.cg_spce b/examples/USER/dpdext/dpdext_tstat/in.cg_spce new file mode 100755 index 0000000000..ea1a3dfcba --- /dev/null +++ b/examples/USER/dpdext/dpdext_tstat/in.cg_spce @@ -0,0 +1,31 @@ +# Coarse-Grained SPC/E Water + +variable T equal 300.0 +variable rc equal 9.0 +variable rcD equal 10.0 + +units real +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +read_data cg_spce.data + +pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 + +pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} + +timestep 1.0 +run_style verlet + +velocity all create ${T} 68768932 + +thermo_style custom step time temp press +thermo 10 + +fix 1 all nve + +run 2000 diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 b/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 new file mode 100644 index 0000000000..6916a5dd6e --- /dev/null +++ b/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 @@ -0,0 +1,293 @@ +LAMMPS (10 Mar 2021) +# Coarse-Grained SPC/E Water + +variable T equal 300.0 +variable rc equal 9.0 +variable rcD equal 10.0 + +units real +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +read_data cg_spce.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2180 atoms + read_data CPU = 0.037 seconds + +pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262 + +pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} +pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 +WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:461) +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10 + +timestep 1.0 +run_style verlet + +velocity all create ${T} 68768932 +velocity all create 300 68768932 + +thermo_style custom step time temp press +thermo 10 + +fix 1 all nve + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 7 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair dpdext/tstat, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 5.380 | 5.380 | 5.380 Mbytes +Step Time Temp Press + 0 0 300 7368.7186 + 10 10 298.34842 6443.6033 + 20 20 303.36187 9303.0158 + 30 30 301.59356 7533.7912 + 40 40 300.97217 5623.9089 + 50 50 300.31652 9105.8093 + 60 60 296.92173 9213.304 + 70 70 294.36593 12701.327 + 80 80 295.30077 6098.4732 + 90 90 296.35396 8051.719 + 100 100 293.72532 5555.983 + 110 110 290.95711 9001.8346 + 120 120 290.91972 10264.241 + 130 130 294.14911 11450.959 + 140 140 299.11994 7244.1639 + 150 150 301.20082 7675.7516 + 160 160 300.71883 9718.1901 + 170 170 295.47176 8931.1414 + 180 180 290.45284 7381.7674 + 190 190 291.66922 11028.436 + 200 200 294.0543 11897.269 + 210 210 299.17955 8939.2171 + 220 220 298.45193 8047.038 + 230 230 300.48548 10033.64 + 240 240 299.24752 6310.7247 + 250 250 304.51487 8710.5626 + 260 260 303.6513 5230.8162 + 270 270 300.76074 12164.773 + 280 280 302.60275 11145.98 + 290 290 297.22957 9521.4384 + 300 300 297.1365 7446.9006 + 310 310 292.18323 8021.8344 + 320 320 295.03958 9130.8594 + 330 330 293.9622 4647.512 + 340 340 290.77751 8001.486 + 350 350 292.34687 11887.668 + 360 360 295.95968 9262.148 + 370 370 293.50476 4181.549 + 380 380 288.69498 7632.071 + 390 390 289.63957 5130.0205 + 400 400 295.02212 5643.5024 + 410 410 296.3944 7267.235 + 420 420 299.22019 7149.9305 + 430 430 298.36689 8384.595 + 440 440 295.33149 10515.75 + 450 450 294.76959 11569.389 + 460 460 300.141 7272.4453 + 470 470 299.14431 7792.5419 + 480 480 302.3697 5837.8675 + 490 490 301.94692 6999.1059 + 500 500 300.25929 4885.3948 + 510 510 302.50013 8231.0438 + 520 520 300.76412 8445.0349 + 530 530 298.5016 9110.432 + 540 540 301.14513 9348.6421 + 550 550 297.36425 10753.314 + 560 560 296.50046 10476.823 + 570 570 300.57267 9889.7968 + 580 580 300.4868 8377.423 + 590 590 296.65103 6859.32 + 600 600 298.50013 7080.5995 + 610 610 300.28274 9502.5438 + 620 620 298.45508 8819.7846 + 630 630 300.24859 6291.4944 + 640 640 299.38719 7430.2366 + 650 650 297.91915 9435.3218 + 660 660 300.61208 6287.9931 + 670 670 303.59291 8357.7639 + 680 680 301.85511 1697.3038 + 690 690 298.96873 5210.2286 + 700 700 298.09035 7510.4359 + 710 710 303.11692 10129.526 + 720 720 302.65473 10488.388 + 730 730 300.15444 7118.5953 + 740 740 300.19245 10582.032 + 750 750 296.73618 6538.0363 + 760 760 299.72857 7588.9487 + 770 770 299.00347 6633.9983 + 780 780 301.38129 8053.5347 + 790 790 298.54819 8711.4965 + 800 800 305.54197 9717.9727 + 810 810 302.96497 7582.0444 + 820 820 306.81537 9433.6446 + 830 830 309.16373 10088.582 + 840 840 313.53881 9509.8624 + 850 850 310.82992 5366.015 + 860 860 306.49798 8499.9157 + 870 870 308.93421 5690.3242 + 880 880 302.56668 5526.3636 + 890 890 306.72501 7380.8469 + 900 900 308.87199 10388.13 + 910 910 312.7367 6613.0734 + 920 920 308.34508 5903.4291 + 930 930 306.39924 8615.6622 + 940 940 310.37544 6849.4694 + 950 950 310.13051 6188.7605 + 960 960 308.68049 7637.532 + 970 970 302.85465 6448.7926 + 980 980 307.40719 8763.0959 + 990 990 304.02815 8373.6518 + 1000 1000 300.69539 5682.6678 + 1010 1010 299.16385 6012.246 + 1020 1020 305.118 7913.4144 + 1030 1030 304.20382 10580.788 + 1040 1040 302.91134 7698.4548 + 1050 1050 298.08593 8952.6724 + 1060 1060 302.56196 10602.997 + 1070 1070 305.98211 12174.358 + 1080 1080 305.70253 12288.219 + 1090 1090 303.22805 7922.7166 + 1100 1100 301.54879 5031.3836 + 1110 1110 302.57611 8547.4189 + 1120 1120 302.00845 12966.595 + 1130 1130 296.10912 4514.1707 + 1140 1140 295.11601 6543.7239 + 1150 1150 287.29188 6453.3386 + 1160 1160 284.83881 7168.9427 + 1170 1170 289.77871 7895.7434 + 1180 1180 293.48011 7680.6885 + 1190 1190 295.69035 8609.6593 + 1200 1200 296.0653 7343.68 + 1210 1210 302.72922 6973.6048 + 1220 1220 304.11805 7322.7664 + 1230 1230 300.24647 6418.2612 + 1240 1240 293.24074 9039.1214 + 1250 1250 300.56214 7877.4055 + 1260 1260 308.03086 5644.2135 + 1270 1270 311.12289 6875.5126 + 1280 1280 307.83182 7204.9894 + 1290 1290 309.58491 9993.2255 + 1300 1300 305.36536 8626.859 + 1310 1310 304.35084 3471.1205 + 1320 1320 304.40125 2149.2701 + 1330 1330 295.74547 6252.9592 + 1340 1340 293.16034 3407.4408 + 1350 1350 298.6302 10139.977 + 1360 1360 300.46627 7312.9011 + 1370 1370 298.00367 2780.8886 + 1380 1380 300.97807 9403.3451 + 1390 1390 294.32612 12005.453 + 1400 1400 296.13403 5569.4907 + 1410 1410 297.86152 9558.6064 + 1420 1420 303.01992 8678.345 + 1430 1430 298.53849 5544.6316 + 1440 1440 293.60633 12879.765 + 1450 1450 296.28813 9312.4229 + 1460 1460 292.64466 8344.5877 + 1470 1470 295.28975 7689.9396 + 1480 1480 300.10761 7436.7346 + 1490 1490 291.6152 8909.6757 + 1500 1500 286.644 9756.5014 + 1510 1510 294.52064 10383.164 + 1520 1520 297.49618 4972.89 + 1530 1530 295.63379 6192.5729 + 1540 1540 295.04528 4987.7191 + 1550 1550 290.41403 7013.6076 + 1560 1560 295.62326 7222.5009 + 1570 1570 299.90584 4282.5688 + 1580 1580 299.04532 7885.433 + 1590 1590 300.03907 5508.0652 + 1600 1600 298.05683 9262.3744 + 1610 1610 297.50015 9544.6913 + 1620 1620 303.21217 6393.6756 + 1630 1630 304.44383 9674.6583 + 1640 1640 302.68977 9065.4408 + 1650 1650 303.62415 6851.1575 + 1660 1660 306.11103 8592.0481 + 1670 1670 300.84566 8483.551 + 1680 1680 303.92882 10113.096 + 1690 1690 305.02534 7389.9402 + 1700 1700 303.52902 5541.9256 + 1710 1710 299.27905 9547.7344 + 1720 1720 294.14366 7269.2402 + 1730 1730 299.49977 8086.0601 + 1740 1740 298.66942 7026.6067 + 1750 1750 296.94428 9595.2435 + 1760 1760 297.36921 6268.7436 + 1770 1770 299.88423 10598.189 + 1780 1780 293.76868 7405.7641 + 1790 1790 297.19444 10837.102 + 1800 1800 296.46054 8345.699 + 1810 1810 299.06801 5256.5992 + 1820 1820 294.17725 5510.7529 + 1830 1830 286.78527 6310.8881 + 1840 1840 284.89686 8249.1144 + 1850 1850 293.79389 4578.9263 + 1860 1860 298.31279 8752.305 + 1870 1870 295.31087 8401.2736 + 1880 1880 298.13297 4354.8694 + 1890 1890 298.90786 11454.088 + 1900 1900 299.1416 9121.4138 + 1910 1910 296.43134 12157.884 + 1920 1920 292.05445 8613.1522 + 1930 1930 300.3421 7898.3626 + 1940 1940 304.55746 6311.259 + 1950 1950 304.03899 8789.3537 + 1960 1960 305.08259 7243.5622 + 1970 1970 304.0858 8712.4796 + 1980 1980 299.14574 5166.3501 + 1990 1990 300.07254 10019.769 + 2000 2000 301.78176 8789.7968 +Loop time of 79.8698 on 1 procs for 2000 steps with 2180 atoms + +Performance: 2.164 ns/day, 11.093 hours/ns, 25.041 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 79.378 | 79.378 | 79.378 | 0.0 | 99.38 +Neigh | 0.22454 | 0.22454 | 0.22454 | 0.0 | 0.28 +Comm | 0.17969 | 0.17969 | 0.17969 | 0.0 | 0.22 +Output | 0.0063846 | 0.0063846 | 0.0063846 | 0.0 | 0.01 +Modify | 0.044496 | 0.044496 | 0.044496 | 0.0 | 0.06 +Other | | 0.03671 | | | 0.05 + +Nlocal: 2180.00 ave 2180 max 2180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6693.00 ave 6693 max 6693 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 261496.0 ave 261496 max 261496 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 261496 +Ave neighs/atom = 119.95229 +Neighbor list builds = 25 +Dangerous builds = 0 +Total wall time: 0:01:20 diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 b/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 new file mode 100644 index 0000000000..890414d580 --- /dev/null +++ b/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 @@ -0,0 +1,293 @@ +LAMMPS (10 Mar 2021) +# Coarse-Grained SPC/E Water + +variable T equal 300.0 +variable rc equal 9.0 +variable rcD equal 10.0 + +units real +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +read_data cg_spce.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2180 atoms + read_data CPU = 0.012 seconds + +pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262 + +pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} +pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 +WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:461) +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10 + +timestep 1.0 +run_style verlet + +velocity all create ${T} 68768932 +velocity all create 300 68768932 + +thermo_style custom step time temp press +thermo 10 + +fix 1 all nve + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 7 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair dpdext/tstat, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes +Step Time Temp Press + 0 0 300 5965.5396 + 10 10 303.16391 8779.1574 + 20 20 306.9014 8268.573 + 30 30 305.84291 9976.0547 + 40 40 301.20527 8832.3902 + 50 50 305.72012 8041.0146 + 60 60 305.1676 7118.8042 + 70 70 305.01132 9423.9307 + 80 80 308.10236 10781.423 + 90 90 309.18703 3637.9961 + 100 100 305.11814 7726.7672 + 110 110 298.37346 8575.1602 + 120 120 304.79786 8910.8048 + 130 130 309.05401 6351.4839 + 140 140 304.28367 4805.137 + 150 150 300.28903 7412.6411 + 160 160 299.39358 10183.593 + 170 170 296.80729 5437.1054 + 180 180 295.2755 8317.0414 + 190 190 303.25949 8338.3453 + 200 200 303.24607 9636.5224 + 210 210 298.56684 10288.264 + 220 220 293.42999 9001.0482 + 230 230 293.12497 9083.5194 + 240 240 291.92847 9659.3388 + 250 250 299.2202 6328.759 + 260 260 297.45209 10405.677 + 270 270 292.12257 7273.9369 + 280 280 289.81113 8957.8747 + 290 290 299.06683 6695.3776 + 300 300 300.75468 6298.5705 + 310 310 296.26524 7432.4815 + 320 320 294.21403 9941.7038 + 330 330 293.01776 4750.2993 + 340 340 295.22553 4968.3595 + 350 350 293.95589 9224.5496 + 360 360 297.94278 8792.0395 + 370 370 298.99075 5453.7814 + 380 380 302.1188 6229.2283 + 390 390 298.48943 8517.5273 + 400 400 295.3701 11328.394 + 410 410 287.74238 4058.0382 + 420 420 288.83732 5706.6773 + 430 430 298.8242 6178.7142 + 440 440 304.42682 10138.321 + 450 450 300.28695 9731.3417 + 460 460 300.34539 9249.4691 + 470 470 303.32231 11638.718 + 480 480 301.46777 4186.402 + 490 490 292.56069 9184.8386 + 500 500 297.26162 11766.733 + 510 510 295.34018 6436.33 + 520 520 300.16314 9325.3669 + 530 530 305.00513 5947.6408 + 540 540 300.88805 5222.7384 + 550 550 301.56707 6669.1808 + 560 560 304.89854 10730.053 + 570 570 299.50424 7956.1042 + 580 580 301.23382 10192.246 + 590 590 298.81222 6017.2125 + 600 600 300.57891 4575.433 + 610 610 301.95936 6309.7515 + 620 620 301.09393 5993.6489 + 630 630 300.47565 4388.7137 + 640 640 299.31886 9535.6093 + 650 650 295.06025 7954.5811 + 660 660 298.72666 8630.7466 + 670 670 302.53833 5636.1305 + 680 680 306.32833 12539.149 + 690 690 296.1951 11345.293 + 700 700 297.00325 6352.1448 + 710 710 298.51181 6922.4379 + 720 720 293.80125 4849.4922 + 730 730 296.52677 11141.583 + 740 740 294.15306 3527.8677 + 750 750 294.74737 8454.0815 + 760 760 292.53913 8187.9032 + 770 770 294.37078 7487.5703 + 780 780 297.50085 9198.7697 + 790 790 298.37773 8969.0024 + 800 800 293.29879 6506.6479 + 810 810 296.58266 8805.7872 + 820 820 290.85616 5248.8123 + 830 830 292.29488 5123.8203 + 840 840 292.77623 8263.5675 + 850 850 297.88225 6777.7444 + 860 860 300.01913 10439.087 + 870 870 295.79578 7318.1322 + 880 880 301.5994 8242.4774 + 890 890 306.63208 8090.6106 + 900 900 303.53759 6831.2666 + 910 910 300.70481 3811.0498 + 920 920 299.96274 8351.1573 + 930 930 299.67435 7046.0534 + 940 940 310.81742 6887.6925 + 950 950 305.09984 4811.088 + 960 960 301.33039 4184.851 + 970 970 301.19205 6417.6542 + 980 980 299.6491 7738.2233 + 990 990 297.33655 9264.0874 + 1000 1000 302.33418 7166.2751 + 1010 1010 300.08402 9121.0882 + 1020 1020 302.82225 6405.7109 + 1030 1030 304.01683 6944.0839 + 1040 1040 305.82618 6160.3838 + 1050 1050 308.12518 4356.0931 + 1060 1060 307.64811 6954.7245 + 1070 1070 313.70509 5558.9804 + 1080 1080 316.09239 7250.6147 + 1090 1090 310.2845 5441.3722 + 1100 1100 300.18899 4417.8774 + 1110 1110 304.02471 5609.1668 + 1120 1120 303.46016 10355.031 + 1130 1130 305.68165 6400.913 + 1140 1140 308.78348 7235.1894 + 1150 1150 299.30025 9246.4856 + 1160 1160 302.70799 9866.9536 + 1170 1170 302.0977 8643.5532 + 1180 1180 307.15407 8866.4664 + 1190 1190 305.78146 7562.4911 + 1200 1200 302.54605 7974.9973 + 1210 1210 306.14264 9554.2381 + 1220 1220 308.89843 6219.5361 + 1230 1230 305.71844 7633.9105 + 1240 1240 306.51911 7705.4795 + 1250 1250 304.78473 8590.5595 + 1260 1260 300.82969 9281.5964 + 1270 1270 305.9271 4951.1323 + 1280 1280 310.32728 9446.3989 + 1290 1290 318.27879 9102.5544 + 1300 1300 310.45777 5931.5457 + 1310 1310 304.81268 1214.4291 + 1320 1320 307.08811 10315.961 + 1330 1330 306.86917 8584.9658 + 1340 1340 307.26912 7254.864 + 1350 1350 310.02754 8508.6256 + 1360 1360 306.12763 4912.6641 + 1370 1370 301.67924 6715.8196 + 1380 1380 298.37239 6149.8821 + 1390 1390 299.62894 8181.4761 + 1400 1400 301.60395 6714.4244 + 1410 1410 297.65752 7035.6575 + 1420 1420 297.02817 7510.2637 + 1430 1430 303.59177 10361.937 + 1440 1440 300.10771 8473.2311 + 1450 1450 291.21837 6097.9954 + 1460 1460 291.58663 7729.0841 + 1470 1470 292.52447 6555.8661 + 1480 1480 294.48264 6960.0201 + 1490 1490 298.34869 8044.2321 + 1500 1500 296.8193 11731.289 + 1510 1510 296.52073 5452.8935 + 1520 1520 294.54819 9591.7969 + 1530 1530 297.36394 5148.5383 + 1540 1540 289.08137 6057.0981 + 1550 1550 288.27007 8965.1965 + 1560 1560 294.84398 8316.9487 + 1570 1570 299.79573 8760.7322 + 1580 1580 295.66745 5045.5322 + 1590 1590 298.14356 7161.1834 + 1600 1600 297.10402 6529.9938 + 1610 1610 299.69137 7741.6027 + 1620 1620 304.93043 11222.109 + 1630 1630 302.01322 10893.107 + 1640 1640 295.47422 8400.3124 + 1650 1650 301.93122 7190.2609 + 1660 1660 305.02639 6140.5552 + 1670 1670 302.86047 8651.5366 + 1680 1680 304.82151 9909.407 + 1690 1690 300.48426 8428.8845 + 1700 1700 293.06643 5333.8144 + 1710 1710 295.43687 9103.4353 + 1720 1720 298.77208 8162.1053 + 1730 1730 300.08189 9603.4371 + 1740 1740 303.16004 10693.291 + 1750 1750 303.54199 9151.023 + 1760 1760 300.99281 4641.2985 + 1770 1770 297.36657 3888.5753 + 1780 1780 298.32969 7286.2299 + 1790 1790 297.34183 8975.8956 + 1800 1800 295.83042 6366.7607 + 1810 1810 295.92044 9308.4953 + 1820 1820 298.10087 7117.2369 + 1830 1830 296.13936 4849.3739 + 1840 1840 296.5869 8321.4011 + 1850 1850 296.74513 9530.6806 + 1860 1860 298.57398 8788.0603 + 1870 1870 299.12825 6015.4777 + 1880 1880 301.91639 11706.441 + 1890 1890 309.85968 10909.493 + 1900 1900 302.64998 8779.8967 + 1910 1910 301.62919 9176.3902 + 1920 1920 300.66238 5369.8681 + 1930 1930 297.64499 8185.09 + 1940 1940 296.47852 10188.803 + 1950 1950 297.802 6679.4466 + 1960 1960 299.78754 7316.8198 + 1970 1970 300.09083 6008.9414 + 1980 1980 297.94119 5615.6403 + 1990 1990 298.37687 9727.308 + 2000 2000 296.08394 6400.2746 +Loop time of 40.5503 on 4 procs for 2000 steps with 2180 atoms + +Performance: 4.261 ns/day, 5.632 hours/ns, 49.321 timesteps/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 37.953 | 38.022 | 38.132 | 1.1 | 93.77 +Neigh | 0.10585 | 0.10835 | 0.10994 | 0.5 | 0.27 +Comm | 2.2287 | 2.3368 | 2.405 | 4.6 | 5.76 +Output | 0.0072037 | 0.0081832 | 0.011022 | 1.8 | 0.02 +Modify | 0.023132 | 0.024188 | 0.025948 | 0.7 | 0.06 +Other | | 0.05032 | | | 0.12 + +Nlocal: 545.000 ave 559 max 531 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 3619.00 ave 3655 max 3594 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +Neighs: 65415.5 ave 66835 max 64310 min +Histogram: 1 0 0 2 0 0 0 0 0 1 + +Total # of neighbors = 261662 +Ave neighs/atom = 120.02844 +Neighbor list builds = 26 +Dangerous builds = 0 +Total wall time: 0:00:40 diff --git a/src/Makefile b/src/Makefile index 679cbe7b97..41d2a91c31 100644 --- a/src/Makefile +++ b/src/Makefile @@ -52,7 +52,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ python qeq replica rigid shock snap spin srd voronoi PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ - user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ + user-diffraction user-dpd user-dpdext user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ diff --git a/src/USER-DPDEXT/README b/src/USER-DPDEXT/README new file mode 100644 index 0000000000..73f8d047f8 --- /dev/null +++ b/src/USER-DPDEXT/README @@ -0,0 +1,10 @@ +Martin Svoboda (ICPF, UJEP) - svobod.martin@gmail.com +Karel Sindelka (ICPF) - sindelka@icpf.cas.cz +Martin Lisal (ICPF, UJEP) - lisal@icpf.cas.cz + +This package implements a generalised force field for dissipative +particle dynamics (DPD). The extension divides contributions +of dissipative and random forces to parrallel and perpendicular parts. +See the doc pages for "pair_style dpdext" and "pair_style dpdext/tstat". + +There are example scripts for using this package in examples/USER/dpdext. diff --git a/src/USER-DPDEXT/pair_dpd_ext.cpp b/src/USER-DPDEXT/pair_dpd_ext.cpp new file mode 100644 index 0000000000..e5405cf071 --- /dev/null +++ b/src/USER-DPDEXT/pair_dpd_ext.cpp @@ -0,0 +1,496 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Kurt Smith (U Pittsburgh) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Martin Svoboda (ICPF, UJEP), Martin LĂ­sal (ICPF, UJEP) +------------------------------------------------------------------------- */ +#include "pair_dpd_ext.h" + +#include +#include "atom.h" +#include "comm.h" +#include "update.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "random_mars.h" +#include "memory.h" +#include "error.h" + + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDExt::PairDPDExt(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; + random = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +PairDPDExt::~PairDPDExt() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(a0); + memory->destroy(gamma); + memory->destroy(gammaT); + memory->destroy(sigma); + memory->destroy(sigmaT); + memory->destroy(ws); + memory->destroy(wsT); + } + + if (random) delete random; +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDExt::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpairx,fpairy,fpairz,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wd,wdPar,wdPerp,randnum,randnumx,randnumy,randnumz,factor_dpd; + double P[3][3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double dtinvsqrt = 1.0/sqrt(update->dt); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + vxtmp = v[i][0]; + vytmp = v[i][1]; + vztmp = v[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + delvx = vxtmp - v[j][0]; + delvy = vytmp - v[j][1]; + delvz = vztmp - v[j][2]; + dot = delx*delvx + dely*delvy + delz*delvz; + + P[0][0] = 1.0 - delx*delx*rinv*rinv; + P[0][1] = - delx*dely*rinv*rinv; + P[0][2] = - delx*delz*rinv*rinv; + + P[1][0] = P[0][1]; + P[1][1] = 1.0 - dely*dely*rinv*rinv; + P[1][2] = - dely*delz*rinv*rinv; + + P[2][0] = P[0][2]; + P[2][1] = P[1][2]; + P[2][2] = 1.0 - delz*delz*rinv*rinv; + + wd = 1.0 - r/cut[itype][jtype]; + wdPar = pow(wd,ws[itype][jtype]); + wdPerp = pow(wd,wsT[itype][jtype]); + + randnum = random->gaussian(); + randnumx = random->gaussian(); + randnumy = random->gaussian(); + randnumz = random->gaussian(); + + // conservative force + fpair = a0[itype][jtype]*wd; + + // drag force - parallel + fpair -= gamma[itype][jtype]*wdPar*wdPar*dot*rinv; + + // random force - parallel + fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; + + fpairx = fpair*rinv*delx; + fpairy = fpair*rinv*dely; + fpairz = fpair*rinv*delz; + + // drag force - perpendicular + fpairx -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[0][0]*delvx + P[0][1]*delvy + P[0][2]*delvz); + fpairy -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[1][0]*delvx + P[1][1]*delvy + P[1][2]*delvz); + fpairz -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[2][0]*delvx + P[2][1]*delvy + P[2][2]*delvz); + + // random force - perpendicular + fpairx += sigmaT[itype][jtype]*wdPerp* + (P[0][0]*randnumx + P[0][1]*randnumy + P[0][2]*randnumz)*dtinvsqrt; + fpairy += sigmaT[itype][jtype]*wdPerp* + (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; + fpairz += sigmaT[itype][jtype]*wdPerp* + (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; + + fpairx *= factor_dpd; + fpairy *= factor_dpd; + fpairz *= factor_dpd; + + f[i][0] += fpairx; + f[i][1] += fpairy; + f[i][2] += fpairz; + if (newton_pair || j < nlocal) { + f[j][0] -= fpairx; + f[j][1] -= fpairy; + f[j][2] -= fpairz; + } + + if (eflag) { + // unshifted eng of conservative term: + // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); + // eng shifted to 0.0 at cutoff + evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd; + evdwl *= factor_dpd; + } + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,0.0, + fpairx, fpairy, fpairz, + delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairDPDExt::allocate() +{ + int i,j; + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (i = 1; i <= n; i++) + for (j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(a0,n+1,n+1,"pair:a0"); + memory->create(gamma,n+1,n+1,"pair:gamma"); + memory->create(gammaT,n+1,n+1,"pair:gammaT"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(sigmaT,n+1,n+1,"pair:sigmaT"); + memory->create(ws,n+1,n+1,"pair:ws"); + memory->create(wsT,n+1,n+1,"pair:wsT"); + for (i = 0; i <= atom->ntypes; i++) + { + for (j = 0; j <= atom->ntypes; j++) + { + sigma[i][j] = gamma[i][j] =sigmaT[i][j] = gammaT[i][j] = 0.0; + ws[i][j] = wsT[i][j] = 1.0; + } + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDPDExt::settings(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR,"Illegal pair_style command"); + + temperature = utils::numeric(FLERR,arg[0],false,lmp); + cut_global = utils::numeric(FLERR,arg[1],false,lmp); + seed = utils::inumeric(FLERR,arg[2],false,lmp); + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0) error->all(FLERR,"Illegal pair_style command"); + delete random; + random = new RanMars(lmp,seed + comm->me); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) { + cut[i][j] = cut_global; + cutsq[i][j] = cut_global*cut_global; + } + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDPDExt::coeff(int narg, char **arg) +{ + if (narg < 7 || narg > 8) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double a0_one = utils::numeric(FLERR,arg[2],false,lmp); + double gamma_one = utils::numeric(FLERR,arg[3],false,lmp); + double gammaT_one = utils::numeric(FLERR,arg[4],false,lmp); + double ws_one = utils::numeric(FLERR,arg[5],false,lmp); + double wsT_one = utils::numeric(FLERR,arg[6],false,lmp); + + double cut_one = cut_global; + if (narg == 8) cut_one = utils::numeric(FLERR,arg[7],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + gamma[i][j] = gamma_one; + gammaT[i][j] = gammaT_one; + ws[i][j] = ws_one; + wsT[i][j] = wsT_one; + cut[i][j] = cut_one; + cutsq[i][j] = cut_one*cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairDPDExt::init_style() +{ + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair dpd requires ghost atoms store velocity"); + + // if newton off, forces between atoms ij will be double computed + // using different random numbers + + if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, + "Pair dpd needs newton pair on for momentum conservation"); + + neighbor->request(this,instance_me); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairDPDExt::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]); + sigmaT[i][j] = sqrt(2.0*force->boltz*temperature*gammaT[i][j]); + + cut[j][i] = cut[i][j]; + cutsq[j][i] = cutsq[i][j]; + a0[j][i] = a0[i][j]; + gamma[j][i] = gamma[i][j]; + gammaT[j][i] = gammaT[i][j]; + sigma[j][i] = sigma[i][j]; + sigmaT[j][i] = sigmaT[i][j]; + ws[j][i] = ws[i][j]; + wsT[j][i] = wsT[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDExt::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&a0[i][j],sizeof(double),1,fp); + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&gammaT[i][j],sizeof(double),1,fp); + fwrite(&ws[i][j],sizeof(double),1,fp); + fwrite(&wsT[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDExt::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&gammaT[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&ws[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&wsT[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gammaT[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&ws[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&wsT[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDExt::write_restart_settings(FILE *fp) +{ + fwrite(&temperature,sizeof(double),1,fp); + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&seed,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDExt::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR,&temperature,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairDPDExt::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g %g\n",i, + a0[i][i],gamma[i][i],gammaT[i][i],ws[i][i],wsT[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairDPDExt::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g %g %g\n",i,j, + a0[i][j],gamma[i][j],gammaT[i][j],ws[i][j],wsT[i][j],cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDExt::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_dpd, double &fforce) +{ + double r,rinv,wd,phi; + + r = sqrt(rsq); + if (r < EPSILON) { + fforce = 0.0; + return 0.0; + } + + rinv = 1.0/r; + wd = 1.0 - r/cut[itype][jtype]; + fforce = a0[itype][jtype]*wd * factor_dpd*rinv; + + phi = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd; + return factor_dpd*phi; +} diff --git a/src/USER-DPDEXT/pair_dpd_ext.h b/src/USER-DPDEXT/pair_dpd_ext.h new file mode 100644 index 0000000000..e85c3451c5 --- /dev/null +++ b/src/USER-DPDEXT/pair_dpd_ext.h @@ -0,0 +1,86 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(dpdext,PairDPDExt) + +#else + +#ifndef LMP_PAIR_DPD_EXT_H +#define LMP_PAIR_DPD_EXT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairDPDExt : public Pair { + public: + PairDPDExt(class LAMMPS *); + virtual ~PairDPDExt(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + void init_style(); + double init_one(int, int); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + virtual void write_data(FILE *); + virtual void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_global,temperature; + int seed; + double **cut; + double **a0,**gamma,**gammaII,**gammaT; + double **sigma,**sigmaT; + double **ws,**wsT; + class RanMars *random; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair dpd requires ghost atoms store velocity + +Use the comm_modify vel yes command to enable this. + +W: Pair dpd needs newton pair on for momentum conservation + +Self-explanatory. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp b/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp new file mode 100644 index 0000000000..bfd10c1374 --- /dev/null +++ b/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp @@ -0,0 +1,376 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Martin Svoboda (ICPF, UJEP), Martin LĂ­sal (ICPF, UJEP) +------------------------------------------------------------------------- */ + +#include "pair_dpd_tstat_ext.h" + +#include +#include "atom.h" +#include "update.h" +#include "force.h" +#include "neigh_list.h" +#include "comm.h" +#include "random_mars.h" +#include "error.h" + + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDTstatExt::PairDPDTstatExt(LAMMPS *lmp) : PairDPDExt(lmp) +{ + single_enable = 0; + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDTstatExt::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,fpairx,fpairy,fpairz,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wd,wdPar,wdPerp,randnum,randnumx,randnumy,randnumz,factor_dpd; + double P[3][3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + ev_init(eflag,vflag); + + // adjust sigma if target T is changing + + if (t_start != t_stop) { + double delta = update->ntimestep - update->beginstep; + if (delta != 0.0) delta /= update->endstep - update->beginstep; + temperature = t_start + delta * (t_stop-t_start); + double boltz = force->boltz; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]); + sigmaT[i][j] = sigmaT[j][i] = sqrt(2.0*boltz*temperature*gammaT[i][j]); + } + } + } + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double dtinvsqrt = 1.0/sqrt(update->dt); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + vxtmp = v[i][0]; + vytmp = v[i][1]; + vztmp = v[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + delvx = vxtmp - v[j][0]; + delvy = vytmp - v[j][1]; + delvz = vztmp - v[j][2]; + dot = delx*delvx + dely*delvy + delz*delvz; + + P[0][0] = 1.0 - delx*delx*rinv*rinv; + P[0][1] = - delx*dely*rinv*rinv; + P[0][2] = - delx*delz*rinv*rinv; + + P[1][0] = P[0][1]; + P[1][1] = 1.0 - dely*dely*rinv*rinv; + P[1][2] = - dely*delz*rinv*rinv; + + P[2][0] = P[0][2]; + P[2][1] = P[1][2]; + P[2][2] = 1.0 - delz*delz*rinv*rinv; + + wd = 1.0 - r/cut[itype][jtype]; + wdPar = pow(wd,ws[itype][jtype]); + wdPerp = pow(wd,wsT[itype][jtype]); + + randnum = random->gaussian(); + randnumx = random->gaussian(); + randnumy = random->gaussian(); + randnumz = random->gaussian(); + + // drag force - parallel + fpair = -gamma[itype][jtype]*wdPar*wdPar*dot*rinv; + + // random force - parallel + fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; + + fpairx = fpair*rinv*delx; + fpairy = fpair*rinv*dely; + fpairz = fpair*rinv*delz; + + // drag force - perpendicular + fpairx -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[0][0]*delvx + P[0][1]*delvy + P[0][2]*delvz); + fpairy -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[1][0]*delvx + P[1][1]*delvy + P[1][2]*delvz); + fpairz -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[2][0]*delvx + P[2][1]*delvy + P[2][2]*delvz); + + // random force - perpendicular + fpairx += sigmaT[itype][jtype]*wdPerp* + (P[0][0]*randnumx + P[0][1]*randnumy + P[0][2]*randnumz)*dtinvsqrt; + fpairy += sigmaT[itype][jtype]*wdPerp* + (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; + fpairz += sigmaT[itype][jtype]*wdPerp* + (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; + + fpairx *= factor_dpd; + fpairy *= factor_dpd; + fpairz *= factor_dpd; + + f[i][0] += fpairx; + f[i][1] += fpairy; + f[i][2] += fpairz; + if (newton_pair || j < nlocal) { + f[j][0] -= fpairx; + f[j][1] -= fpairy; + f[j][2] -= fpairz; + } + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + 0.0,0.0, + fpairx, fpairy, fpairz, + delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::settings(int narg, char **arg) +{ + if (narg != 4) error->all(FLERR,"Illegal pair_style command"); + + t_start = utils::numeric(FLERR,arg[0],false,lmp); + t_stop = utils::numeric(FLERR,arg[1],false,lmp); + cut_global = utils::numeric(FLERR,arg[2],false,lmp); + seed = utils::inumeric(FLERR,arg[3],false,lmp); + + temperature = t_start; + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0) error->all(FLERR,"Illegal pair_style command"); + delete random; + random = new RanMars(lmp,seed + comm->me); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::coeff(int narg, char **arg) +{ + if (narg < 6 || narg > 7) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double a0_one = 0.0; + double gamma_one = utils::numeric(FLERR,arg[2],false,lmp); + double gammaT_one = utils::numeric(FLERR,arg[3],false,lmp); + double ws_one = utils::numeric(FLERR,arg[4],false,lmp); + double wsT_one = utils::numeric(FLERR,arg[5],false,lmp); + + double cut_one = cut_global; + if (narg == 7) cut_one = utils::numeric(FLERR,arg[6],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + gamma[i][j] = gamma_one; + gammaT[i][j] = gammaT_one; + ws[i][j] = ws_one; + wsT[i][j] = wsT_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&gammaT[i][j],sizeof(double),1,fp); + fwrite(&ws[i][j],sizeof(double),1,fp); + fwrite(&wsT[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&gammaT[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&ws[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&wsT[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gammaT[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&ws[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&wsT[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::write_restart_settings(FILE *fp) +{ + fwrite(&t_start,sizeof(double),1,fp); + fwrite(&t_stop,sizeof(double),1,fp); + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&seed,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR,&t_start,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&t_stop,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&t_start,1,MPI_DOUBLE,0,world); + MPI_Bcast(&t_stop,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + + temperature = t_start; + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g\n",i,gamma[i][i],gammaT[i][i],ws[i][i],wsT[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g %g\n",i,j, + gamma[i][j],gammaT[i][j],ws[i][j],wsT[i][j],cut[i][j]); +} diff --git a/src/USER-DPDEXT/pair_dpd_tstat_ext.h b/src/USER-DPDEXT/pair_dpd_tstat_ext.h new file mode 100644 index 0000000000..c8441f90bd --- /dev/null +++ b/src/USER-DPDEXT/pair_dpd_tstat_ext.h @@ -0,0 +1,62 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(dpdext/tstat,PairDPDTstatExt) + +#else + +#ifndef LMP_PAIR_DPD_TSTAT_EXT_H +#define LMP_PAIR_DPD_TSTAT_EXT_H + +#include "pair_dpd_ext.h" + +namespace LAMMPS_NS { + +class PairDPDTstatExt : public PairDPDExt { + public: + PairDPDTstatExt(class LAMMPS *); + ~PairDPDTstatExt() {} + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + + protected: + double t_start,t_stop; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/ From 4041a07e6670ba1dbd089665e5252e3fcb36dc35 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 16 Apr 2021 15:43:03 +0200 Subject: [PATCH 02/12] add USER-DPDEXT to CMakeLists.txt --- cmake/CMakeLists.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index f567a15d25..d840dedf6c 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -120,9 +120,9 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF - USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DPDEXT USER-DRUDE USER-EFF USER-FEP + USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC + USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE) From ce51305b2d0559b3d31c67fc9fa8e8541721a224 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 16 Apr 2021 15:44:20 +0200 Subject: [PATCH 03/12] fix typing error in doc file --- doc/src/pair_dpdext.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/pair_dpdext.rst b/doc/src/pair_dpdext.rst index 301f9f3ea0..4b6855774d 100644 --- a/doc/src/pair_dpdext.rst +++ b/doc/src/pair_dpdext.rst @@ -52,7 +52,7 @@ of 3 terms f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ w(r) = & 1 - r/r_c \\ -where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\a` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. +where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. For the style *dpdext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. From 62f7e9731690fcd7c0b5bf2b5d715a19cde917be Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 14:39:55 +0200 Subject: [PATCH 04/12] rename pair_styles --- src/USER-DPDEXT/pair_dpd_ext.h | 2 +- ...d_tstat_ext.cpp => pair_dpd_ext_tstat.cpp} | 22 +++++++++---------- ...r_dpd_tstat_ext.h => pair_dpd_ext_tstat.h} | 12 +++++----- 3 files changed, 18 insertions(+), 18 deletions(-) rename src/USER-DPDEXT/{pair_dpd_tstat_ext.cpp => pair_dpd_ext_tstat.cpp} (95%) rename src/USER-DPDEXT/{pair_dpd_tstat_ext.h => pair_dpd_ext_tstat.h} (86%) diff --git a/src/USER-DPDEXT/pair_dpd_ext.h b/src/USER-DPDEXT/pair_dpd_ext.h index e85c3451c5..fabb95b773 100644 --- a/src/USER-DPDEXT/pair_dpd_ext.h +++ b/src/USER-DPDEXT/pair_dpd_ext.h @@ -13,7 +13,7 @@ #ifdef PAIR_CLASS -PairStyle(dpdext,PairDPDExt) +PairStyle(dpd/ext,PairDPDExt) #else diff --git a/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp b/src/USER-DPDEXT/pair_dpd_ext_tstat.cpp similarity index 95% rename from src/USER-DPDEXT/pair_dpd_tstat_ext.cpp rename to src/USER-DPDEXT/pair_dpd_ext_tstat.cpp index bfd10c1374..5449ca7358 100644 --- a/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp +++ b/src/USER-DPDEXT/pair_dpd_ext_tstat.cpp @@ -15,7 +15,7 @@ Contributing authors: Martin Svoboda (ICPF, UJEP), Martin LĂ­sal (ICPF, UJEP) ------------------------------------------------------------------------- */ -#include "pair_dpd_tstat_ext.h" +#include "pair_dpd_ext_tstat.h" #include #include "atom.h" @@ -33,7 +33,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairDPDTstatExt::PairDPDTstatExt(LAMMPS *lmp) : PairDPDExt(lmp) +PairDPDExtTstat::PairDPDExtTstat(LAMMPS *lmp) : PairDPDExt(lmp) { single_enable = 0; writedata = 1; @@ -41,7 +41,7 @@ PairDPDTstatExt::PairDPDTstatExt(LAMMPS *lmp) : PairDPDExt(lmp) /* ---------------------------------------------------------------------- */ -void PairDPDTstatExt::compute(int eflag, int vflag) +void PairDPDExtTstat::compute(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,fpairx,fpairy,fpairz,fpair; @@ -190,7 +190,7 @@ void PairDPDTstatExt::compute(int eflag, int vflag) global settings ------------------------------------------------------------------------- */ -void PairDPDTstatExt::settings(int narg, char **arg) +void PairDPDExtTstat::settings(int narg, char **arg) { if (narg != 4) error->all(FLERR,"Illegal pair_style command"); @@ -221,7 +221,7 @@ void PairDPDTstatExt::settings(int narg, char **arg) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairDPDTstatExt::coeff(int narg, char **arg) +void PairDPDExtTstat::coeff(int narg, char **arg) { if (narg < 6 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients"); @@ -261,7 +261,7 @@ void PairDPDTstatExt::coeff(int narg, char **arg) proc 0 writes to restart file ------------------------------------------------------------------------- */ -void PairDPDTstatExt::write_restart(FILE *fp) +void PairDPDExtTstat::write_restart(FILE *fp) { write_restart_settings(fp); @@ -283,7 +283,7 @@ void PairDPDTstatExt::write_restart(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void PairDPDTstatExt::read_restart(FILE *fp) +void PairDPDExtTstat::read_restart(FILE *fp) { read_restart_settings(fp); @@ -316,7 +316,7 @@ void PairDPDTstatExt::read_restart(FILE *fp) proc 0 writes to restart file ------------------------------------------------------------------------- */ -void PairDPDTstatExt::write_restart_settings(FILE *fp) +void PairDPDExtTstat::write_restart_settings(FILE *fp) { fwrite(&t_start,sizeof(double),1,fp); fwrite(&t_stop,sizeof(double),1,fp); @@ -329,7 +329,7 @@ void PairDPDTstatExt::write_restart_settings(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void PairDPDTstatExt::read_restart_settings(FILE *fp) +void PairDPDExtTstat::read_restart_settings(FILE *fp) { if (comm->me == 0) { utils::sfread(FLERR,&t_start,sizeof(double),1,fp,nullptr,error); @@ -357,7 +357,7 @@ void PairDPDTstatExt::read_restart_settings(FILE *fp) proc 0 writes to data file ------------------------------------------------------------------------- */ -void PairDPDTstatExt::write_data(FILE *fp) +void PairDPDExtTstat::write_data(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) fprintf(fp,"%d %g %g %g %g\n",i,gamma[i][i],gammaT[i][i],ws[i][i],wsT[i][i]); @@ -367,7 +367,7 @@ void PairDPDTstatExt::write_data(FILE *fp) proc 0 writes all pairs to data file ------------------------------------------------------------------------- */ -void PairDPDTstatExt::write_data_all(FILE *fp) +void PairDPDExtTstat::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) diff --git a/src/USER-DPDEXT/pair_dpd_tstat_ext.h b/src/USER-DPDEXT/pair_dpd_ext_tstat.h similarity index 86% rename from src/USER-DPDEXT/pair_dpd_tstat_ext.h rename to src/USER-DPDEXT/pair_dpd_ext_tstat.h index c8441f90bd..23cdd1d3c7 100644 --- a/src/USER-DPDEXT/pair_dpd_tstat_ext.h +++ b/src/USER-DPDEXT/pair_dpd_ext_tstat.h @@ -13,21 +13,21 @@ #ifdef PAIR_CLASS -PairStyle(dpdext/tstat,PairDPDTstatExt) +PairStyle(dpd/ext/tstat,PairDPDExtTstat) #else -#ifndef LMP_PAIR_DPD_TSTAT_EXT_H -#define LMP_PAIR_DPD_TSTAT_EXT_H +#ifndef LMP_PAIR_DPD_EXT_TSTAT_H +#define LMP_PAIR_DPD_EXT_TSTAT_H #include "pair_dpd_ext.h" namespace LAMMPS_NS { -class PairDPDTstatExt : public PairDPDExt { +class PairDPDExtTstat : public PairDPDExt { public: - PairDPDTstatExt(class LAMMPS *); - ~PairDPDTstatExt() {} + PairDPDExtTstat(class LAMMPS *); + ~PairDPDExtTstat() {} void compute(int, int); void settings(int, char **); void coeff(int, char **); From 2e63d126e3a2b2c5f966bd0abd46a72fe99c3831 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 15:49:11 +0200 Subject: [PATCH 05/12] change dir to MISC --- examples/USER/{dpdext => misc/dpd_ext}/README | 0 .../dpd_ext}/dpdext/dpdext.data | 0 .../{dpdext => misc/dpd_ext}/dpdext/in.dpdext | 2 +- .../dpd_ext}/dpdext/log.10Mar21.dpdext.g++.1 | 28 +++++++------- .../dpd_ext}/dpdext/log.10Mar21.dpdext.g++.4 | 30 +++++++-------- .../dpd_ext}/dpdext_tstat/cg_spce.data | 0 .../dpd_ext}/dpdext_tstat/cg_spce_table.pot | 0 .../dpd_ext}/dpdext_tstat/in.cg_spce | 4 +- .../dpdext_tstat/log.10Mar21.dpdext.g++.1 | 38 +++++++++---------- .../dpdext_tstat/log.10Mar21.dpdext.g++.4 | 38 +++++++++---------- src/USER-DPDEXT/README | 10 ----- src/USER-MISC/README | 2 + .../pair_dpd_ext.cpp | 0 src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext.h | 0 .../pair_dpd_ext_tstat.cpp | 0 .../pair_dpd_ext_tstat.h | 0 16 files changed, 72 insertions(+), 80 deletions(-) rename examples/USER/{dpdext => misc/dpd_ext}/README (100%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext/dpdext.data (100%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext/in.dpdext (92%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext/log.10Mar21.dpdext.g++.1 (91%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext/log.10Mar21.dpdext.g++.4 (90%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/cg_spce.data (100%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/cg_spce_table.pot (100%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/in.cg_spce (76%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/log.10Mar21.dpdext.g++.1 (91%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/log.10Mar21.dpdext.g++.4 (91%) delete mode 100644 src/USER-DPDEXT/README rename src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext.cpp (100%) rename src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext.h (100%) rename src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext_tstat.cpp (100%) rename src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext_tstat.h (100%) diff --git a/examples/USER/dpdext/README b/examples/USER/misc/dpd_ext/README similarity index 100% rename from examples/USER/dpdext/README rename to examples/USER/misc/dpd_ext/README diff --git a/examples/USER/dpdext/dpdext/dpdext.data b/examples/USER/misc/dpd_ext/dpdext/dpdext.data similarity index 100% rename from examples/USER/dpdext/dpdext/dpdext.data rename to examples/USER/misc/dpd_ext/dpdext/dpdext.data diff --git a/examples/USER/dpdext/dpdext/in.dpdext b/examples/USER/misc/dpd_ext/dpdext/in.dpdext similarity index 92% rename from examples/USER/dpdext/dpdext/in.dpdext rename to examples/USER/misc/dpd_ext/dpdext/in.dpdext index 3101be9a1c..726f3a7b39 100755 --- a/examples/USER/dpdext/dpdext/in.dpdext +++ b/examples/USER/misc/dpd_ext/dpdext/in.dpdext @@ -23,7 +23,7 @@ mass 1 1.0 mass 2 2.0 ### -pair_style dpdext ${T} ${rc} 3854262 +pair_style dpd/ext ${T} ${rc} 3854262 pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 similarity index 91% rename from examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 rename to examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 index ef61ed11b8..862aea77af 100644 --- a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 +++ b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (10 Mar 2021) +LAMMPS (8 Apr 2021) # DPD Fluid variable T equal 1.0 @@ -34,9 +34,9 @@ mass 1 1.0 mass 2 2.0 ### -pair_style dpdext ${T} ${rc} 3854262 -pair_style dpdext 1 ${rc} 3854262 -pair_style dpdext 1 1 3854262 +pair_style dpd/ext ${T} ${rc} 3854262 +pair_style dpd/ext 1 ${rc} 3854262 +pair_style dpd/ext 1 1 3854262 pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} @@ -61,7 +61,7 @@ Neighbor list info ... ghost atom cutoff = 1.52 binsize = 0.76, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair dpdext, perpetual + (1) pair dpd/ext, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton @@ -169,20 +169,20 @@ Step Time Temp Press 49000 490 1.0337198 7.5777833 49500 495 0.94052507 7.3661443 50000 500 0.98527818 7.1746325 -Loop time of 10.2559 on 1 procs for 50000 steps with 200 atoms +Loop time of 9.88248 on 1 procs for 50000 steps with 200 atoms -Performance: 4212216.548 tau/day, 4875.251 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 4371371.882 tau/day, 5059.458 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 8.9888 | 8.9888 | 8.9888 | 0.0 | 87.65 -Neigh | 0.832 | 0.832 | 0.832 | 0.0 | 8.11 -Comm | 0.30913 | 0.30913 | 0.30913 | 0.0 | 3.01 -Output | 0.0021966 | 0.0021966 | 0.0021966 | 0.0 | 0.02 -Modify | 0.084161 | 0.084161 | 0.084161 | 0.0 | 0.82 -Other | | 0.03957 | | | 0.39 +Pair | 8.7028 | 8.7028 | 8.7028 | 0.0 | 88.06 +Neigh | 0.73687 | 0.73687 | 0.73687 | 0.0 | 7.46 +Comm | 0.31881 | 0.31881 | 0.31881 | 0.0 | 3.23 +Output | 0.0013947 | 0.0013947 | 0.0013947 | 0.0 | 0.01 +Modify | 0.081394 | 0.081394 | 0.081394 | 0.0 | 0.82 +Other | | 0.04118 | | | 0.42 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 similarity index 90% rename from examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 rename to examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 index bbbf47a46c..12b35ecf53 100644 --- a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 +++ b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (10 Mar 2021) +LAMMPS (8 Apr 2021) # DPD Fluid variable T equal 1.0 @@ -34,9 +34,9 @@ mass 1 1.0 mass 2 2.0 ### -pair_style dpdext ${T} ${rc} 3854262 -pair_style dpdext 1 ${rc} 3854262 -pair_style dpdext 1 1 3854262 +pair_style dpd/ext ${T} ${rc} 3854262 +pair_style dpd/ext 1 ${rc} 3854262 +pair_style dpd/ext 1 1 3854262 pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} @@ -61,7 +61,7 @@ Neighbor list info ... ghost atom cutoff = 1.52 binsize = 0.76, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair dpdext, perpetual + (1) pair dpd/ext, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton @@ -169,20 +169,20 @@ Step Time Temp Press 49000 490 0.9759139 7.4839858 49500 495 0.91538068 7.1780491 50000 500 1.0310634 7.1522794 -Loop time of 9.14414 on 4 procs for 50000 steps with 200 atoms +Loop time of 8.5908 on 4 procs for 50000 steps with 200 atoms -Performance: 4724338.550 tau/day, 5467.984 timesteps/s -96.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 5028633.375 tau/day, 5820.178 timesteps/s +95.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.0824 | 5.212 | 5.3376 | 5.1 | 57.00 -Neigh | 0.49498 | 0.50029 | 0.505 | 0.6 | 5.47 -Comm | 3.1637 | 3.2822 | 3.4143 | 6.3 | 35.89 -Output | 0.0025831 | 0.003088 | 0.004569 | 1.5 | 0.03 -Modify | 0.067261 | 0.068927 | 0.070535 | 0.5 | 0.75 -Other | | 0.07762 | | | 0.85 +Pair | 4.9505 | 5.054 | 5.1885 | 4.1 | 58.83 +Neigh | 0.47025 | 0.47603 | 0.47954 | 0.5 | 5.54 +Comm | 2.7876 | 2.9237 | 3.0336 | 5.5 | 34.03 +Output | 0.0024114 | 0.0029766 | 0.0046443 | 1.8 | 0.03 +Modify | 0.062911 | 0.064188 | 0.065603 | 0.4 | 0.75 +Other | | 0.06992 | | | 0.81 Nlocal: 50.0000 ave 53 max 46 min Histogram: 1 0 0 0 1 0 0 0 1 1 @@ -198,4 +198,4 @@ Dangerous builds = 5000 write_data final.data pair ij System init for write_data ... -Total wall time: 0:00:09 +Total wall time: 0:00:08 diff --git a/examples/USER/dpdext/dpdext_tstat/cg_spce.data b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data similarity index 100% rename from examples/USER/dpdext/dpdext_tstat/cg_spce.data rename to examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data diff --git a/examples/USER/dpdext/dpdext_tstat/cg_spce_table.pot b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot similarity index 100% rename from examples/USER/dpdext/dpdext_tstat/cg_spce_table.pot rename to examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot diff --git a/examples/USER/dpdext/dpdext_tstat/in.cg_spce b/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce similarity index 76% rename from examples/USER/dpdext/dpdext_tstat/in.cg_spce rename to examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce index ea1a3dfcba..b93dc3eec5 100755 --- a/examples/USER/dpdext/dpdext_tstat/in.cg_spce +++ b/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce @@ -13,10 +13,10 @@ comm_modify vel yes read_data cg_spce.data -pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262 pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD} timestep 1.0 run_style verlet diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 similarity index 91% rename from examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 rename to examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 index 6916a5dd6e..8f75dfa917 100644 --- a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 +++ b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (10 Mar 2021) +LAMMPS (8 Apr 2021) # Coarse-Grained SPC/E Water variable T equal 300.0 @@ -18,19 +18,19 @@ Reading data file ... 1 by 1 by 1 MPI processor grid reading atoms ... 2180 atoms - read_data CPU = 0.037 seconds + read_data CPU = 0.020 seconds -pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262 pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:461) -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10 +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10 timestep 1.0 run_style verlet @@ -56,7 +56,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard - (2) pair dpdext/tstat, perpetual, copy from (1) + (2) pair dpd/ext/tstat, perpetual, copy from (1) attributes: half, newton on pair build: copy stencil: none @@ -264,20 +264,20 @@ Step Time Temp Press 1980 1980 299.14574 5166.3501 1990 1990 300.07254 10019.769 2000 2000 301.78176 8789.7968 -Loop time of 79.8698 on 1 procs for 2000 steps with 2180 atoms +Loop time of 91.2059 on 1 procs for 2000 steps with 2180 atoms -Performance: 2.164 ns/day, 11.093 hours/ns, 25.041 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.895 ns/day, 12.667 hours/ns, 21.928 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 79.378 | 79.378 | 79.378 | 0.0 | 99.38 -Neigh | 0.22454 | 0.22454 | 0.22454 | 0.0 | 0.28 -Comm | 0.17969 | 0.17969 | 0.17969 | 0.0 | 0.22 -Output | 0.0063846 | 0.0063846 | 0.0063846 | 0.0 | 0.01 -Modify | 0.044496 | 0.044496 | 0.044496 | 0.0 | 0.06 -Other | | 0.03671 | | | 0.05 +Pair | 90.668 | 90.668 | 90.668 | 0.0 | 99.41 +Neigh | 0.23231 | 0.23231 | 0.23231 | 0.0 | 0.25 +Comm | 0.20819 | 0.20819 | 0.20819 | 0.0 | 0.23 +Output | 0.0049558 | 0.0049558 | 0.0049558 | 0.0 | 0.01 +Modify | 0.052906 | 0.052906 | 0.052906 | 0.0 | 0.06 +Other | | 0.03904 | | | 0.04 Nlocal: 2180.00 ave 2180 max 2180 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -290,4 +290,4 @@ Total # of neighbors = 261496 Ave neighs/atom = 119.95229 Neighbor list builds = 25 Dangerous builds = 0 -Total wall time: 0:01:20 +Total wall time: 0:01:31 diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 similarity index 91% rename from examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 rename to examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 index 890414d580..278aba0687 100644 --- a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 +++ b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (10 Mar 2021) +LAMMPS (8 Apr 2021) # Coarse-Grained SPC/E Water variable T equal 300.0 @@ -18,19 +18,19 @@ Reading data file ... 1 by 2 by 2 MPI processor grid reading atoms ... 2180 atoms - read_data CPU = 0.012 seconds + read_data CPU = 0.005 seconds -pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262 pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:461) -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10 +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10 timestep 1.0 run_style verlet @@ -56,7 +56,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard - (2) pair dpdext/tstat, perpetual, copy from (1) + (2) pair dpd/ext/tstat, perpetual, copy from (1) attributes: half, newton on pair build: copy stencil: none @@ -264,20 +264,20 @@ Step Time Temp Press 1980 1980 297.94119 5615.6403 1990 1990 298.37687 9727.308 2000 2000 296.08394 6400.2746 -Loop time of 40.5503 on 4 procs for 2000 steps with 2180 atoms +Loop time of 41.5171 on 4 procs for 2000 steps with 2180 atoms -Performance: 4.261 ns/day, 5.632 hours/ns, 49.321 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 4.162 ns/day, 5.766 hours/ns, 48.173 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 37.953 | 38.022 | 38.132 | 1.1 | 93.77 -Neigh | 0.10585 | 0.10835 | 0.10994 | 0.5 | 0.27 -Comm | 2.2287 | 2.3368 | 2.405 | 4.6 | 5.76 -Output | 0.0072037 | 0.0081832 | 0.011022 | 1.8 | 0.02 -Modify | 0.023132 | 0.024188 | 0.025948 | 0.7 | 0.06 -Other | | 0.05032 | | | 0.12 +Pair | 38.667 | 38.954 | 39.453 | 4.8 | 93.83 +Neigh | 0.10947 | 0.11039 | 0.11153 | 0.3 | 0.27 +Comm | 1.8661 | 2.3644 | 2.652 | 19.6 | 5.70 +Output | 0.0082644 | 0.0094232 | 0.01281 | 2.0 | 0.02 +Modify | 0.024678 | 0.025206 | 0.025888 | 0.3 | 0.06 +Other | | 0.05335 | | | 0.13 Nlocal: 545.000 ave 559 max 531 min Histogram: 1 0 0 0 1 1 0 0 0 1 @@ -290,4 +290,4 @@ Total # of neighbors = 261662 Ave neighs/atom = 120.02844 Neighbor list builds = 26 Dangerous builds = 0 -Total wall time: 0:00:40 +Total wall time: 0:00:41 diff --git a/src/USER-DPDEXT/README b/src/USER-DPDEXT/README deleted file mode 100644 index 73f8d047f8..0000000000 --- a/src/USER-DPDEXT/README +++ /dev/null @@ -1,10 +0,0 @@ -Martin Svoboda (ICPF, UJEP) - svobod.martin@gmail.com -Karel Sindelka (ICPF) - sindelka@icpf.cas.cz -Martin Lisal (ICPF, UJEP) - lisal@icpf.cas.cz - -This package implements a generalised force field for dissipative -particle dynamics (DPD). The extension divides contributions -of dissipative and random forces to parrallel and perpendicular parts. -See the doc pages for "pair_style dpdext" and "pair_style dpdext/tstat". - -There are example scripts for using this package in examples/USER/dpdext. diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 314fe6146e..3e2c8ed000 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -90,6 +90,8 @@ pair_style coul/slater/long, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 Fe pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 pair_style e3b, Steven Strong (U Chicago), stevene.strong at gmail dot com, 16 Apr 19 pair_style drip, Mingjian Wen, University of Minnesota, wenxx151 at umn.edu, 17 Apr 19 +pair_style dpd/ext, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP, svobod.martin at gmail dot com, 23 Apr 21 +pair_style dpd/ext/tstat, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP , svobod.martin at gmail dot com, 23 Apr 21 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 diff --git a/src/USER-DPDEXT/pair_dpd_ext.cpp b/src/USER-MISC/pair_dpd_ext.cpp similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext.cpp rename to src/USER-MISC/pair_dpd_ext.cpp diff --git a/src/USER-DPDEXT/pair_dpd_ext.h b/src/USER-MISC/pair_dpd_ext.h similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext.h rename to src/USER-MISC/pair_dpd_ext.h diff --git a/src/USER-DPDEXT/pair_dpd_ext_tstat.cpp b/src/USER-MISC/pair_dpd_ext_tstat.cpp similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext_tstat.cpp rename to src/USER-MISC/pair_dpd_ext_tstat.cpp diff --git a/src/USER-DPDEXT/pair_dpd_ext_tstat.h b/src/USER-MISC/pair_dpd_ext_tstat.h similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext_tstat.h rename to src/USER-MISC/pair_dpd_ext_tstat.h From 3ac2b369938e24c5dfc081a15bf374235db21d68 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 16:10:00 +0200 Subject: [PATCH 06/12] add link to Commands_pair.rst --- doc/src/Commands_pair.rst | 2 ++ examples/USER/misc/dpd_ext/dpdext/dpdext.data | 0 examples/USER/misc/dpd_ext/dpdext/in.dpdext | 0 examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data | 0 examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot | 0 examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce | 0 6 files changed, 2 insertions(+) mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext/dpdext.data mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext/in.dpdext mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index b91a749364..15126d6d34 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -87,6 +87,8 @@ OPT. * :doc:`coul/wolf/cs ` * :doc:`dpd (gio) ` * :doc:`dpd/fdt ` + * :doc:`dpd/ext ` + * :doc:`dpd/ext/tstat ` * :doc:`dpd/fdt/energy (k) ` * :doc:`dpd/tstat (go) ` * :doc:`dsmc ` diff --git a/examples/USER/misc/dpd_ext/dpdext/dpdext.data b/examples/USER/misc/dpd_ext/dpdext/dpdext.data old mode 100755 new mode 100644 diff --git a/examples/USER/misc/dpd_ext/dpdext/in.dpdext b/examples/USER/misc/dpd_ext/dpdext/in.dpdext old mode 100755 new mode 100644 diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data old mode 100755 new mode 100644 diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot old mode 100755 new mode 100644 diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce b/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce old mode 100755 new mode 100644 From e28867eed0e440ac0e56f06fbd6948c2d74a23a2 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 20:08:56 +0200 Subject: [PATCH 07/12] change doc --- doc/src/Commands_pair.rst | 4 ++-- doc/src/{pair_dpdext.rst => pair_dpd_ext.rst} | 0 doc/src/pair_style.rst | 2 ++ 3 files changed, 4 insertions(+), 2 deletions(-) rename doc/src/{pair_dpdext.rst => pair_dpd_ext.rst} (100%) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 15126d6d34..40b81a2fd1 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -87,8 +87,8 @@ OPT. * :doc:`coul/wolf/cs ` * :doc:`dpd (gio) ` * :doc:`dpd/fdt ` - * :doc:`dpd/ext ` - * :doc:`dpd/ext/tstat ` + * :doc:`dpd/ext ` + * :doc:`dpd/ext/tstat ` * :doc:`dpd/fdt/energy (k) ` * :doc:`dpd/tstat (go) ` * :doc:`dsmc ` diff --git a/doc/src/pair_dpdext.rst b/doc/src/pair_dpd_ext.rst similarity index 100% rename from doc/src/pair_dpdext.rst rename to doc/src/pair_dpd_ext.rst diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 4990674973..94d4e07486 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -150,6 +150,8 @@ accelerated styles exist. * :doc:`coul/wolf ` - Coulomb via Wolf potential * :doc:`coul/wolf/cs ` - Coulomb via Wolf potential with core/shell adjustments * :doc:`dpd ` - dissipative particle dynamics (DPD) +* :doc:`dpd/ext ` - generalised force field for DPD +* :doc:`dpd/ext/tstat ` - pair-wise DPD thermostatting with generalised force field * :doc:`dpd/fdt ` - DPD for constant temperature and pressure * :doc:`dpd/fdt/energy ` - DPD for constant energy and enthalpy * :doc:`dpd/tstat ` - pair-wise DPD thermostatting From a9abcadc018ebbc49eb6c75f06d22133a7224bd6 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 20:09:41 +0200 Subject: [PATCH 08/12] one more doc fix --- doc/src/pair_dpd_ext.rst | 43 ++++++++++++++++++++-------------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index 4b6855774d..cfc72fe84c 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -1,9 +1,10 @@ -.. index:: pair_style dpdext +.. index:: pair_style dpd/ext +.. index:: pair_style dpd/ext/tstat -pair_style dpdext command +pair_style dpd/ext command ========================== -pair_style dpdext/tstat command +pair_style dpd/ext/tstat command ================================ Syntax @@ -12,8 +13,8 @@ Syntax .. code-block:: LAMMPS - pair_style dpdext T cutoff seed - pair_style dpdext/tstat Tstart Tstop cutoff seed + pair_style dpd/ext T cutoff seed + pair_style dpd/ext/tstat Tstart Tstop cutoff seed * T = temperature (temperature units) * Tstart,Tstop = desired temperature at start/end of run (temperature units) @@ -26,22 +27,22 @@ Examples .. code-block:: LAMMPS - pair_style dpdext 1.0 2.5 34387 + pair_style dpd/ext 1.0 2.5 34387 pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2 pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2 - pair_style dpdext/tstat 1.0 1.0 2.5 34387 + pair_style dpd/ext/tstat 1.0 1.0 2.5 34387 pair_coeff 1 1 4.5 4.5 0.5 0.5 1.2 pair_coeff 1 2 4.5 4.5 0.5 0.5 1.2 Description """"""""""" -The style *dpdext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. +The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. -Style *dpdext/tstat* invokes an extended DPD thermostat on pairwise interactions, which is equivalent to the non-conservative portion of the extended DPD force field. To use *dpdext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. +Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. -For the style *dpdext*\ , the force on atom I due to atom J is given as a sum +For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum of 3 terms .. math:: @@ -54,15 +55,15 @@ of 3 terms where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. -For the style *dpdext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. -For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. +For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. -For the style *dpdext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. -For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. +For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. -For the style *dpdext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: +For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: * A (force units) * :math:`\gamma_{\perp}` (force/velocity units) @@ -74,7 +75,7 @@ For the style *dpdext*, the following coefficients must be defined for each pair The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. -For the style *dpdext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. +For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. .. note:: @@ -89,17 +90,17 @@ For the style *dpdext/tstat*, the coefficients defined for each pair of atoms ty **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The style *dpdext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. +The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. The pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`. -The :doc:`pair_modify ` table option is not relevant for the style *dpdext*. +The :doc:`pair_modify ` table option is not relevant for the style *dpd/ext*. -The style *dpdext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. +The style *dpd/ext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. The pair styles can only be used via the pair keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords. -The style *dpdext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. +The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. ---------- @@ -107,7 +108,7 @@ The style *dpdext/tstat* can ramp its target temperature over multiple runs, usi Restrictions """""""""""" -The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpdext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. +The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. The pair styles require to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. From 1f24a45ef7a32a7c62f28dd5a4043d9dddbe1d47 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 20:09:51 +0200 Subject: [PATCH 09/12] fix Makefile --- src/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makefile b/src/Makefile index 4fcc7402c9..d5f0e600d6 100644 --- a/src/Makefile +++ b/src/Makefile @@ -52,7 +52,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ python qeq replica rigid shock snap spin srd voronoi PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ - user-diffraction user-dpd user-dpdext user-drude user-eff user-fep user-h5md \ + user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-pace user-plumed user-ptm user-qmmm \ From 628b06b7deb9b0b4824c397a00170b37e8ea2834 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 20:15:11 +0200 Subject: [PATCH 10/12] fix CMakeLists.txt --- cmake/CMakeLists.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index d840dedf6c..f567a15d25 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -120,9 +120,9 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DPDEXT USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC - USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF + USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE) From d60c630e56ef458929c5800020f2856fc078684d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 15:05:06 -0400 Subject: [PATCH 11/12] cosmetic changes: whitespace and include file order --- src/USER-MISC/pair_dpd_ext.cpp | 30 ++++++++++++++-------------- src/USER-MISC/pair_dpd_ext_tstat.cpp | 22 ++++++++++---------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/src/USER-MISC/pair_dpd_ext.cpp b/src/USER-MISC/pair_dpd_ext.cpp index e5405cf071..ee03a6d1b9 100644 --- a/src/USER-MISC/pair_dpd_ext.cpp +++ b/src/USER-MISC/pair_dpd_ext.cpp @@ -20,17 +20,17 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_ext.h" -#include #include "atom.h" #include "comm.h" -#include "update.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "random_mars.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" +#include using namespace LAMMPS_NS; @@ -126,23 +126,23 @@ void PairDPDExt::compute(int eflag, int vflag) delvy = vytmp - v[j][1]; delvz = vztmp - v[j][2]; dot = delx*delvx + dely*delvy + delz*delvz; - + P[0][0] = 1.0 - delx*delx*rinv*rinv; P[0][1] = - delx*dely*rinv*rinv; P[0][2] = - delx*delz*rinv*rinv; - + P[1][0] = P[0][1]; P[1][1] = 1.0 - dely*dely*rinv*rinv; P[1][2] = - dely*delz*rinv*rinv; - + P[2][0] = P[0][2]; P[2][1] = P[1][2]; P[2][2] = 1.0 - delz*delz*rinv*rinv; - + wd = 1.0 - r/cut[itype][jtype]; wdPar = pow(wd,ws[itype][jtype]); wdPerp = pow(wd,wsT[itype][jtype]); - + randnum = random->gaussian(); randnumx = random->gaussian(); randnumy = random->gaussian(); @@ -156,7 +156,7 @@ void PairDPDExt::compute(int eflag, int vflag) // random force - parallel fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; - + fpairx = fpair*rinv*delx; fpairy = fpair*rinv*dely; fpairz = fpair*rinv*delz; @@ -176,7 +176,7 @@ void PairDPDExt::compute(int eflag, int vflag) (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; fpairz += sigmaT[itype][jtype]*wdPerp* (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; - + fpairx *= factor_dpd; fpairy *= factor_dpd; fpairz *= factor_dpd; @@ -190,7 +190,7 @@ void PairDPDExt::compute(int eflag, int vflag) f[j][2] -= fpairz; } - if (eflag) { + if (eflag) { // unshifted eng of conservative term: // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); // eng shifted to 0.0 at cutoff diff --git a/src/USER-MISC/pair_dpd_ext_tstat.cpp b/src/USER-MISC/pair_dpd_ext_tstat.cpp index 5449ca7358..a9f66fb38c 100644 --- a/src/USER-MISC/pair_dpd_ext_tstat.cpp +++ b/src/USER-MISC/pair_dpd_ext_tstat.cpp @@ -17,15 +17,15 @@ #include "pair_dpd_ext_tstat.h" -#include #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" #include "force.h" #include "neigh_list.h" -#include "comm.h" #include "random_mars.h" -#include "error.h" +#include "update.h" +#include using namespace LAMMPS_NS; @@ -114,23 +114,23 @@ void PairDPDExtTstat::compute(int eflag, int vflag) delvy = vytmp - v[j][1]; delvz = vztmp - v[j][2]; dot = delx*delvx + dely*delvy + delz*delvz; - + P[0][0] = 1.0 - delx*delx*rinv*rinv; P[0][1] = - delx*dely*rinv*rinv; P[0][2] = - delx*delz*rinv*rinv; - + P[1][0] = P[0][1]; P[1][1] = 1.0 - dely*dely*rinv*rinv; P[1][2] = - dely*delz*rinv*rinv; - + P[2][0] = P[0][2]; P[2][1] = P[1][2]; P[2][2] = 1.0 - delz*delz*rinv*rinv; - + wd = 1.0 - r/cut[itype][jtype]; wdPar = pow(wd,ws[itype][jtype]); wdPerp = pow(wd,wsT[itype][jtype]); - + randnum = random->gaussian(); randnumx = random->gaussian(); randnumy = random->gaussian(); @@ -141,7 +141,7 @@ void PairDPDExtTstat::compute(int eflag, int vflag) // random force - parallel fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; - + fpairx = fpair*rinv*delx; fpairy = fpair*rinv*dely; fpairz = fpair*rinv*delz; @@ -161,7 +161,7 @@ void PairDPDExtTstat::compute(int eflag, int vflag) (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; fpairz += sigmaT[itype][jtype]*wdPerp* (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; - + fpairx *= factor_dpd; fpairy *= factor_dpd; fpairz *= factor_dpd; From 8fc9eb26bc6025b0849c4c64eef459d835feff58 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 15:08:20 -0400 Subject: [PATCH 12/12] address spell checker warnings --- doc/src/pair_style.rst | 4 ++-- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 94d4e07486..ce74b0d873 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -150,8 +150,8 @@ accelerated styles exist. * :doc:`coul/wolf ` - Coulomb via Wolf potential * :doc:`coul/wolf/cs ` - Coulomb via Wolf potential with core/shell adjustments * :doc:`dpd ` - dissipative particle dynamics (DPD) -* :doc:`dpd/ext ` - generalised force field for DPD -* :doc:`dpd/ext/tstat ` - pair-wise DPD thermostatting with generalised force field +* :doc:`dpd/ext ` - generalized force field for DPD +* :doc:`dpd/ext/tstat ` - pair-wise DPD thermostatting with generalized force field * :doc:`dpd/fdt ` - DPD for constant temperature and pressure * :doc:`dpd/fdt/energy ` - DPD for constant energy and enthalpy * :doc:`dpd/tstat ` - pair-wise DPD thermostatting diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index da0617ce91..c29ff2b1d1 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2538,6 +2538,7 @@ ppn pppm prd Prakash +Praprotnik pre Pre prec