diff --git a/doc/src/Eqs/fix_gcmc1.jpg b/doc/src/Eqs/fix_gcmc1.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..158cf8b61f98390acfc353032e882e26fdbcf8a3
Binary files /dev/null and b/doc/src/Eqs/fix_gcmc1.jpg differ
diff --git a/doc/src/Eqs/fix_gcmc1.tex b/doc/src/Eqs/fix_gcmc1.tex
new file mode 100644
index 0000000000000000000000000000000000000000..c4b0d6252705298b9868f265c6bceb2679e46b94
--- /dev/null
+++ b/doc/src/Eqs/fix_gcmc1.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mu &=&\mu^{id} + \mu^{ex}
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/fix_gcmc2.jpg b/doc/src/Eqs/fix_gcmc2.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..d054f584305d763e5b7baa8881a1f1a0d96f0a62
Binary files /dev/null and b/doc/src/Eqs/fix_gcmc2.jpg differ
diff --git a/doc/src/Eqs/fix_gcmc2.tex b/doc/src/Eqs/fix_gcmc2.tex
new file mode 100644
index 0000000000000000000000000000000000000000..fc4d90355dd6911f4cc4b8b61d09b243e5a87b68
--- /dev/null
+++ b/doc/src/Eqs/fix_gcmc2.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mu^{id} &=& k T \ln{\rho \Lambda^3} \\
+&=& k T \ln{\frac{\phi P \Lambda^3}{k T}}
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/fix_gcmc3.jpg b/doc/src/Eqs/fix_gcmc3.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..e87764afd9181dd6c4707c0a33b0a80abd2170d0
Binary files /dev/null and b/doc/src/Eqs/fix_gcmc3.jpg differ
diff --git a/doc/src/Eqs/fix_gcmc3.tex b/doc/src/Eqs/fix_gcmc3.tex
new file mode 100644
index 0000000000000000000000000000000000000000..6aac2b9e1fd028e2c25816d253ebc3cda3a8c120
--- /dev/null
+++ b/doc/src/Eqs/fix_gcmc3.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\Lambda &=& \sqrt{ \frac{h^2}{2 \pi m k T}}
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 802cf2c4adc28bac4a9e53e2cd9c46be8d3044b4..f4637e776d6d3ab5ca2365cc0bb8f682e8f880dd 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -40,8 +40,11 @@ field.
NOTE: The newer {charmmfsh} style was released in March 2017. We
recommend it be used instead of the older {charmm} style when running
-a simulation with the CHARMM force field. See the discussion below
-and more details on the "pair_style charmm"_pair_charmm.html doc page.
+a simulation with the CHARMM force field and Coulomb cutoffs, via the
+"pair_style lj/charmmfsw/coul/charmmfsh"_pair_charmm.html command.
+Otherwise the older {charmm} style is fine to use. See the discussion
+below and more details on the "pair_style charmm"_pair_charmm.html doc
+page.
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
@@ -82,13 +85,18 @@ special_bonds 1-4 scaling factor to 0.0 (which is the
default). Otherwise 1-4 non-bonded interactions in dihedrals will be
computed twice.
-For simulations using the CHARMM force field, the difference between
-the {charmm} and {charmmfsh} styles is in the computation of the 1-4
-non-bond interactions, if the distance between the two atoms is within
-the switching distance of the pairwise potential defined by the
-corresponding CHARMM pair style, i.e. between the inner and outer
-cutoffs specified for the pair style. See the discussion on the
-"CHARMM pair_style"_pair_charmm.html doc page for details.
+For simulations using the CHARMM force field with a Coulomb cutoff,
+the difference between the {charmm} and {charmmfsh} styles is in the
+computation of the 1-4 non-bond interactions, though only if the
+distance between the two atoms is within the switching region of the
+pairwise potential defined by the corresponding CHARMM pair style,
+i.e. between the inner and outer cutoffs specified for the pair style.
+The {charmmfsh} style should only be used when using the "pair_style
+lj/charmmfsw/coul/charmmfsh"_pair_charmm.html to make the Coulombic
+pairwise calculations consistent. Use the {charmm} style with
+long-range Coulombics or the older "pair_style
+lj/charmm/coul/charmm"_pair_charmm.html command. See the discussion
+on the "CHARMM pair_style"_pair_charmm.html doc page for details.
Note that for AMBER force fields, which use pair styles with "lj/cut",
the special_bonds 1-4 scaling factor should be set to the AMBER
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index 1a419628e9dc896fcd7f7b6eea12af8ab805008b..723e0ec6d9899585faedbce58478e65e4b8600e7 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -122,11 +122,11 @@ If used with "fix nvt"_fix_nh.html, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature
used in fix nvt. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation cell. Also,
-it is important that the temperature used by fix nvt be dynamic,
+it is important that the temperature used by fix nvt be dynamic/dof,
which can be achieved as follows:
compute mdtemp mdatoms temp
-compute_modify mdtemp dynamic yes
+compute_modify mdtemp dynamic/dof yes
fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
fix_modify mdnvt temp mdtemp :pre
@@ -204,10 +204,43 @@ atoms/molecules are assigned to two groups: the default group "all"
and the group specified in the fix gcmc command (which can also be
"all").
-The gas reservoir pressure can be specified using the {pressure}
+The chemical potential is a user-specified input parameter defined
+as:
+
+:c,image(Eqs/fix_gcmc1.jpg)
+
+The second term mu_ex is the excess chemical potential due to
+energetic interactions and is formally zero for the fictitious gas
+reservoir but is non-zero for interacting systems. So, while the chemical
+potential of the reservoir and the simulation cell are equal, mu_ex is not,
+and as a result, the densities of the two are generally quite different.
+The first term mu_id is the ideal gas contribution to the chemical potential.
+mu_id can be related to the density or pressure of the fictitious gas reservoir by:
+
+:c,image(Eqs/fix_gcmc2.jpg)
+
+where k is Boltzman's constant,
+T is the user-specified temperature, rho is the number density,
+P is the pressure, and phi is the fugacity coefficient.
+The constant Lambda is required for dimensional consistency.
+For all unit styles except {lj} it is defined as the thermal
+de Broglie wavelength
+
+:c,image(Eqs/fix_gcmc3.jpg)
+
+where h is Planck's constant, and m is the mass of the exchanged atom or molecule.
+For unit style {lj}, Lambda is simply set to the unity. Note that prior to March 2017
+Lambda for unit style {lj} was calculated using the above formula with h set to
+the rather specific value of 0.18292026. Chemical potential
+under the old definition can be converted to an equivalent value under the new
+definition by subtracting 3kTln(Lambda_old).
+
+As an alternative to specifying mu directly, the ideal gas reservoir
+can be defined by its pressure P using the {pressure}
keyword, in which case the user-specified chemical potential is
-ignored. For non-ideal gas reservoirs, the user may also specify the
-fugacity coefficient using the {fugacity_coeff} keyword.
+ignored. The user may also specify the
+fugacity coefficient phi using the {fugacity_coeff} keyword, which
+defaults to unity.
The {full_energy} option means that fix GCMC will compute the total
potential energy of the entire simulated system. The total system
@@ -224,7 +257,8 @@ potential energy calculations, including the following:
many-body pair styles
hybrid pair styles
eam pair styles
- triclinic systems
+ tail corrections
+
need to include potential energy contributions from other fixes :ul
In these cases, LAMMPS will automatically apply the {full_energy}
@@ -276,6 +310,13 @@ therefore, you will want to use the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:
+NOTE: If the density of the cell is initially very small or zero,
+and increases to a much larger density after a period of equilibration,
+then certain quantities that are only calculated once at the start
+(kspace parameters, tail corrections) may no longer be accurate.
+The solution is to start a new simulation after the equilibrium
+density has been reached.
+
With some pair_styles, such as "Buckingham"_pair_buck.html,
"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reax_c.html,
two atoms placed close to each other may have an arbitrary large,
@@ -366,7 +407,7 @@ referenced by the user for each subsequent fix gcmc command.
[Default:]
The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
-and full_energy = no,
+fugacity_coeff = 1, and full_energy = no,
except for the situations where full_energy is required, as
listed above.
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index e1101b4174e14a56bc91ea80849e97544b8074af..94954a222670b2a8d004acfe4ebad732cb27f272 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -84,9 +84,9 @@ CHARMM force field.
The styles with {charmm} (not {charmmfsw} or {charmmfsh}) in their
name are the older, original LAMMPS implementations. They compute the
LJ and Coulombic interactions with an energy switching function (esw,
-a cubic polynomial, shown in the formula below), which ramps the
-energy smoothly to zero between the inner and outer cutoff. This can
-cause irregularities in pair-wise forces (due to the discontinuous 2nd
+shown in the formula below as S(r)), which ramps the energy smoothly
+to zero between the inner and outer cutoff. This can cause
+irregularities in pair-wise forces (due to the discontinuous 2nd
derivative of energy at the boundaries of the switching region), which
in some cases can result in detectable artifacts in an MD simulation.
diff --git a/examples/gcmc/in.gcmc.lj b/examples/gcmc/in.gcmc.lj
index 9b1f465f045ce2dc52e9880e326e4cde26bbf2a3..fc9afdb7f837d07984516421ff6e4bb8a5cef9ab 100644
--- a/examples/gcmc/in.gcmc.lj
+++ b/examples/gcmc/in.gcmc.lj
@@ -1,18 +1,23 @@
# GCMC for LJ simple fluid, no dynamics
+# T = 2.0
+# rho ~ 0.5
+# p ~ 1.5
+# mu_ex ~ 0.0
+# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
-# variables available on command line
+# variables modifiable using -var command line switch
-variable mu index -21.0
-variable disp index 1.0
+variable mu index -1.25
variable temp index 2.0
-variable lbox index 10.0
+variable disp index 1.0
+variable lbox index 5.0
# global model settings
units lj
atom_style atomic
-pair_style lj/cut 3.0
-pair_modify tail yes
+pair_style lj/cut 3.0
+pair_modify tail no # turn of to avoid triggering full_energy
# box
@@ -28,15 +33,27 @@ mass * 1.0
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
+# averaging
+
+variable rho equal density
+variable p equal press
+variable nugget equal 1.0e-8
+variable lambda equal 1.0
+variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
+fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
+variable rhoav equal f_ave[1]
+variable pav equal f_ave[2]
+variable muexav equal f_ave[3]
+
# output
-variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
+variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
+variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
compute_modify thermo_temp dynamic yes
-thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc
-thermo 100
+thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+thermo 1000
# run
-run 1000
+run 10000
diff --git a/examples/gcmc/log.24Mar17.gcmc.lj.g++.1 b/examples/gcmc/log.24Mar17.gcmc.lj.g++.1
index 5f967192e47dac52a4db4ead6e120bccc79fa62e..36a9fe885d82cea983da3026bc098eb2725dc4ac 100644
--- a/examples/gcmc/log.24Mar17.gcmc.lj.g++.1
+++ b/examples/gcmc/log.24Mar17.gcmc.lj.g++.1
@@ -1,28 +1,35 @@
LAMMPS (17 Mar 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
+# T = 2.0
+# rho ~ 0.5
+# p ~ 1.5
+# mu_ex ~ 0.0
+# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
-# variables available on command line
+# variables modifiable using -var command line switch
-variable mu index -21.0
-variable disp index 1.0
+variable mu index -1.25
variable temp index 2.0
-variable lbox index 10.0
+variable disp index 1.0
+variable lbox index 5.0
# global model settings
units lj
atom_style atomic
pair_style lj/cut 3.0
-pair_modify tail yes
+pair_modify tail no # turn of to avoid triggering full_energy
# box
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
-region box block 0 10.0 0 ${lbox} 0 ${lbox}
-region box block 0 10.0 0 10.0 0 ${lbox}
-region box block 0 10.0 0 10.0 0 10.0
+region box block 0 5.0 0 ${lbox} 0 ${lbox}
+region box block 0 5.0 0 5.0 0 ${lbox}
+region box block 0 5.0 0 5.0 0 5.0
create_box 1 box
-Created orthogonal box = (0 0 0) to (10 10 10)
+Created orthogonal box = (0 0 0) to (5 5 5)
1 by 1 by 1 MPI processor grid
# lj parameters
@@ -34,70 +41,89 @@ mass * 1.0
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 1.0
+fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
+fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
+
+# averaging
+
+variable rho equal density
+variable p equal press
+variable nugget equal 1.0e-8
+variable lambda equal 1.0
+variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
+variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
+variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
+variable muex equal -1.25-2.0*ln(density*1+${nugget})
+variable muex equal -1.25-2.0*ln(density*1+1e-08)
+fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
+variable rhoav equal f_ave[1]
+variable pav equal f_ave[2]
+variable muexav equal f_ave[3]
# output
-variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
+variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
+variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
+variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
+variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
+variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
compute_modify thermo_temp dynamic yes
-thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc
-thermo 100
+thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+thermo 1000
# run
-run 1000
+run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
- binsize = 1.65, bins = 7 7 7
+ binsize = 1.65, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 0.4369 | 0.4369 | 0.4369 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc
- 0 0 0 0 -0 0 0 0 0 0
- 100 1.9042848 0.39026453 -1.7692765 2.8466449 0.292 292 0.3619855 0.30247792 0.40278761
- 200 1.8651924 0.47815517 -1.8494955 2.7886155 0.305 305 0.34021109 0.30357196 0.37759189
- 300 2.0626994 0.52068504 -1.8197295 3.0834166 0.291 291 0.32055605 0.3003043 0.36103862
- 400 2.0394818 0.53751435 -1.7636699 3.0482184 0.278 278 0.31698808 0.29995864 0.35441275
- 500 1.9628066 0.54594742 -1.7145336 2.9339513 0.287 287 0.31211861 0.29724228 0.35161407
- 600 1.9845913 0.40846162 -1.8199325 2.9669308 0.299 299 0.30976643 0.29612711 0.34933559
- 700 1.8582606 0.53445462 -1.7869306 2.777974 0.296 296 0.30642103 0.29446478 0.34633665
- 800 2.0340641 0.66057698 -1.7075279 3.0403148 0.283 283 0.30730979 0.29746793 0.34768045
- 900 2.0830765 0.63731971 -1.894775 3.114911 0.322 322 0.30636338 0.29737705 0.34737644
- 1000 1.9688933 0.50024802 -1.7013944 2.9428299 0.281 281 0.3053174 0.29772245 0.34788254
-Loop time of 3.98286 on 1 procs for 1000 steps with 281 atoms
-
-Performance: 108464.750 tau/day, 251.076 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+ 0 0 0 0 -0 0 0 0 0 0 0 0 0
+ 1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219
+ 2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004
+ 3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537
+ 4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657
+ 5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777
+ 6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359
+ 7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399
+ 8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766
+ 9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544
+ 10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094
+Loop time of 13.05 on 1 procs for 10000 steps with 60 atoms
+
+Performance: 331035.016 tau/day, 766.285 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.10563 | 0.10563 | 0.10563 | 0.0 | 2.65
-Neigh | 0.33428 | 0.33428 | 0.33428 | 0.0 | 8.39
-Comm | 0.027969 | 0.027969 | 0.027969 | 0.0 | 0.70
-Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.00
-Modify | 3.5096 | 3.5096 | 3.5096 | 0.0 | 88.12
-Other | | 0.005197 | | | 0.13
-
-Nlocal: 281 ave 281 max 281 min
+Pair | 0.37239 | 0.37239 | 0.37239 | 0.0 | 2.85
+Neigh | 0.94764 | 0.94764 | 0.94764 | 0.0 | 7.26
+Comm | 0.092473 | 0.092473 | 0.092473 | 0.0 | 0.71
+Output | 0.00023365 | 0.00023365 | 0.00023365 | 0.0 | 0.00
+Modify | 11.627 | 11.627 | 11.627 | 0.0 | 89.09
+Other | | 0.01054 | | | 0.08
+
+Nlocal: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 977 ave 977 max 977 min
+Nghost: 663 ave 663 max 663 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5902 ave 5902 max 5902 min
+Neighs: 2133 ave 2133 max 2133 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 5902
-Ave neighs/atom = 21.0036
-Neighbor list builds = 1000
+Total # of neighbors = 2133
+Ave neighs/atom = 35.55
+Neighbor list builds = 10000
Dangerous builds = 0
-Total wall time: 0:00:03
+Total wall time: 0:00:13
diff --git a/examples/gcmc/log.24Mar17.gcmc.lj.g++.4 b/examples/gcmc/log.24Mar17.gcmc.lj.g++.4
index db4cc7fd9ac95c5dc2188f036e45341c7d1b574f..8694d8b95e940268768011a600d6847299a3783b 100644
--- a/examples/gcmc/log.24Mar17.gcmc.lj.g++.4
+++ b/examples/gcmc/log.24Mar17.gcmc.lj.g++.4
@@ -1,28 +1,35 @@
LAMMPS (17 Mar 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
+# T = 2.0
+# rho ~ 0.5
+# p ~ 1.5
+# mu_ex ~ 0.0
+# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
-# variables available on command line
+# variables modifiable using -var command line switch
-variable mu index -21.0
-variable disp index 1.0
+variable mu index -1.25
variable temp index 2.0
-variable lbox index 10.0
+variable disp index 1.0
+variable lbox index 5.0
# global model settings
units lj
atom_style atomic
pair_style lj/cut 3.0
-pair_modify tail yes
+pair_modify tail no # turn of to avoid triggering full_energy
# box
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
-region box block 0 10.0 0 ${lbox} 0 ${lbox}
-region box block 0 10.0 0 10.0 0 ${lbox}
-region box block 0 10.0 0 10.0 0 10.0
+region box block 0 5.0 0 ${lbox} 0 ${lbox}
+region box block 0 5.0 0 5.0 0 ${lbox}
+region box block 0 5.0 0 5.0 0 5.0
create_box 1 box
-Created orthogonal box = (0 0 0) to (10 10 10)
+Created orthogonal box = (0 0 0) to (5 5 5)
1 by 2 by 2 MPI processor grid
# lj parameters
@@ -34,70 +41,89 @@ mass * 1.0
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 1.0
+fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
+fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
+
+# averaging
+
+variable rho equal density
+variable p equal press
+variable nugget equal 1.0e-8
+variable lambda equal 1.0
+variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
+variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
+variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
+variable muex equal -1.25-2.0*ln(density*1+${nugget})
+variable muex equal -1.25-2.0*ln(density*1+1e-08)
+fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
+variable rhoav equal f_ave[1]
+variable pav equal f_ave[2]
+variable muexav equal f_ave[3]
# output
-variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
+variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
+variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
+variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
+variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
+variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
compute_modify thermo_temp dynamic yes
-thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc
-thermo 100
+thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+thermo 1000
# run
-run 1000
+run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
- binsize = 1.65, bins = 7 7 7
+ binsize = 1.65, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 0.434 | 0.434 | 0.434 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc
- 0 0 0 0 -0 0 0 0 0 0
- 100 2.0328045 0.58661762 -1.6812724 3.0385824 0.287 287 0.35917318 0.30067507 0.38663622
- 200 1.9594279 0.50682399 -1.7308396 2.9287927 0.284 284 0.33788365 0.30337335 0.37300293
- 300 2.0602937 0.7028247 -1.9278541 3.0806296 0.315 315 0.31882007 0.29697498 0.36167185
- 400 1.995183 0.4328246 -1.8715454 2.983026 0.307 307 0.31527654 0.29681901 0.35673374
- 500 2.1390101 0.48232215 -1.554138 3.1960306 0.257 257 0.31372975 0.30003067 0.35558858
- 600 2.0584244 0.4929049 -1.6995569 3.0767263 0.283 283 0.31114213 0.29801665 0.35160109
- 700 1.9155066 0.49654243 -1.5770611 2.8624174 0.265 265 0.31056419 0.29944173 0.35157337
- 800 2.0883562 0.52731947 -1.8261112 3.1220925 0.3 300 0.30730979 0.29704354 0.34898892
- 900 2.0470677 0.5605993 -2.0130053 3.0610656 0.322 322 0.30484441 0.29586719 0.34678883
- 1000 2.004135 0.50642204 -1.6956257 2.9955798 0.283 283 0.30396929 0.29634309 0.34770304
-Loop time of 3.688 on 4 procs for 1000 steps with 283 atoms
-
-Performance: 117136.751 tau/day, 271.150 timesteps/s
-99.2% CPU use with 4 MPI tasks x no OpenMP threads
+Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+ 0 0 0 0 -0 0 0 0 0 0 0 0 0
+ 1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866
+ 2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794
+ 3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578
+ 4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078
+ 5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867
+ 6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549
+ 7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793
+ 8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191
+ 9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837
+ 10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238
+Loop time of 13.0611 on 4 procs for 10000 steps with 69 atoms
+
+Performance: 330753.007 tau/day, 765.632 timesteps/s
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.024644 | 0.026027 | 0.027483 | 0.6 | 0.71
-Neigh | 0.085449 | 0.088998 | 0.092893 | 0.9 | 2.41
-Comm | 0.045756 | 0.051296 | 0.056578 | 1.7 | 1.39
-Output | 0.00028491 | 0.00030857 | 0.00035262 | 0.0 | 0.01
-Modify | 3.5189 | 3.5191 | 3.5194 | 0.0 | 95.42
-Other | | 0.002221 | | | 0.06
-
-Nlocal: 70.75 ave 77 max 68 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-Nghost: 514.25 ave 520 max 507 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-Neighs: 1483.5 ave 1715 max 1359 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-
-Total # of neighbors = 5934
-Ave neighs/atom = 20.9682
-Neighbor list builds = 1000
+Pair | 0.08888 | 0.09443 | 0.099889 | 1.4 | 0.72
+Neigh | 0.27721 | 0.28532 | 0.29177 | 1.1 | 2.18
+Comm | 0.27648 | 0.28875 | 0.30268 | 1.9 | 2.21
+Output | 0.00029635 | 0.00043058 | 0.00048113 | 0.0 | 0.00
+Modify | 12.384 | 12.384 | 12.384 | 0.0 | 94.82
+Other | | 0.008055 | | | 0.06
+
+Nlocal: 17.25 ave 23 max 10 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Nghost: 506.5 ave 519 max 490 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs: 705.75 ave 998 max 369 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 2823
+Ave neighs/atom = 40.913
+Neighbor list builds = 10000
Dangerous builds = 0
-Total wall time: 0:00:03
+Total wall time: 0:00:13
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index a7483a1d00c1b4a6483e22f7a8501121f1c5a31a..407c980729d12f16aa579e9442ff6e412142f11f 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -432,7 +432,8 @@ void FixGCMC::init()
(force->pair == NULL) ||
(force->pair->single_enable == 0) ||
(force->pair_match("hybrid",0)) ||
- (force->pair_match("eam",0))
+ (force->pair_match("eam",0)) ||
+ (force->pair->tail_flag)
) {
full_flag = true;
if (comm->me == 0)
@@ -618,13 +619,18 @@ void FixGCMC::init()
}
// compute beta, lambda, sigma, and the zz factor
-
+ // For LJ units, lambda=1
beta = 1.0/(force->boltz*reservoir_temperature);
- double lambda = sqrt(force->hplanck*force->hplanck/
- (2.0*MY_PI*gas_mass*force->mvv2e*
+ if (strcmp(update->unit_style,"lj") == 0)
+ zz = exp(beta*chemical_potential);
+ else {
+ double lambda = sqrt(force->hplanck*force->hplanck/
+ (2.0*MY_PI*gas_mass*force->mvv2e*
force->boltz*reservoir_temperature));
+ zz = exp(beta*chemical_potential)/(pow(lambda,3.0));
+ }
+
sigma = sqrt(force->boltz*reservoir_temperature*tfac_insert/gas_mass/force->mvv2e);
- zz = exp(beta*chemical_potential)/(pow(lambda,3.0));
if (pressure_flag) zz = pressure*fugacity_coeff*beta/force->nktv2p;
imagezero = ((imageint) IMGMAX << IMG2BITS) |
diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp
index 2fac8e40df5756decae59dbc195b04a957496aec..e66b7c9fc2ac34bf80e197461b8ea9314c7320c4 100644
--- a/src/USER-MANIFOLD/fix_manifoldforce.cpp
+++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp
@@ -84,8 +84,8 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,msg);
}
- *(ptr_m->get_params()) = new double[nvars];
- if( ptr_m->get_params() == NULL ){
+ ptr_m->params = new double[nvars];
+ if( ptr_m->params == NULL ){
error->all(FLERR,"Parameter pointer was NULL!");
}
@@ -94,7 +94,7 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) :
// and sets the values of those arguments that were _not_
// equal style vars (so that they are not overwritten each time step).
- double *params = *(ptr_m->get_params());
+ double *params = ptr_m->params;
for( int i = 0; i < nvars; ++i ){
if( was_var( arg[i+4] ) )
error->all(FLERR,"Equal-style variables not allowed with fix manifoldforce");
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
index e27762a7d590cb45b6302501abc0835272308879..0d48e145e03b2ce4d60a8b1e5f449d43282a1167 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@@ -131,11 +131,11 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg,
strcpy( tstrs[i], arg[i+6] + offset );
}
- *ptr_m->get_params() = new double[nvars];
- if( !(*ptr_m->get_params()) ) error->all(FLERR,"Failed to allocate params!");
+ ptr_m->params = new double[nvars];
+ if( !ptr_m->params ) error->all(FLERR,"Failed to allocate params!");
for( int i = 0; i < nvars; ++i ){
// If param i was variable type, it will be set later...
- (*ptr_m->get_params())[i] = is_var[i] ? 0.0 : force->numeric( FLERR, arg[i+6] );
+ ptr_m->params[i] = is_var[i] ? 0.0 : force->numeric( FLERR, arg[i+6] );
}
ptr_m->post_param_init();
@@ -262,6 +262,7 @@ void FixNVEManifoldRattle::init()
void FixNVEManifoldRattle::update_var_params()
{
+
if( nevery > 0 ){
stats.x_iters = 0;
stats.v_iters = 0;
@@ -270,7 +271,8 @@ void FixNVEManifoldRattle::update_var_params()
stats.v_iters_per_atom = 0.0;
}
- double **ptr_params = ptr_m->get_params();
+ double *ptr_params = ptr_m->params;
+
for( int i = 0; i < nvars; ++i ){
if( is_var[i] ){
tvars[i] = input->variable->find(tstrs[i]);
@@ -281,8 +283,8 @@ void FixNVEManifoldRattle::update_var_params()
if( input->variable->equalstyle(tvars[i]) ){
tstyle[i] = EQUAL;
double new_val = input->variable->compute_equal(tvars[i]);
- // fprintf( stdout, "New value of var %d is now %f\n", i+1, new_val );
- *(ptr_params[i]) = new_val;
+
+ ptr_params[i] = new_val;
}else{
error->all(FLERR,
"Variable for fix nve/manifold/rattle is invalid style");
diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h
index 85692a8b6b8cd0110941877fd4e6405ed855f143..d0ffa214ac4b0bd11fa6334f534c0d4c71377a50 100644
--- a/src/USER-MANIFOLD/manifold.h
+++ b/src/USER-MANIFOLD/manifold.h
@@ -63,12 +63,12 @@ namespace user_manifold {
virtual void set_atom_id( tagint a_id ){}
virtual int nparams() = 0;
- double **get_params(){ return ¶ms; };
+ // double *get_params(){ return params; };
// Overload if any initialization depends on params:
virtual void post_param_init(){}
virtual void checkup(){} // Some diagnostics...
- protected:
+
double *params;
};
diff --git a/src/update.cpp b/src/update.cpp
index 35492006ccbe0c0dd451a7ea092db36b521ffa40..5599dc6c88492ea2fcfdf8f61b44f71a8d11108f 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -128,7 +128,7 @@ void Update::set_units(const char *style)
if (strcmp(style,"lj") == 0) {
force->boltz = 1.0;
- force->hplanck = 0.18292026; // using LJ parameters for argon
+ force->hplanck = 1.0;
force->mvv2e = 1.0;
force->ftm2v = 1.0;
force->mv2d = 1.0;