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Merge branch 'master' into fix-compiler-warnings

This commit is contained in:
Axel Kohlmeyer 2019-10-25 14:07:50 -04:00
parent e7cb2f4cac 33b14891ab
commit 22288e06b7
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GPG Key ID: D9B44E93BF0C375A
237 changed files with 6899 additions and 6429 deletions
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2
cmake/CMakeLists.txt
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@ -53,7 +53,7 @@ include(CheckCCompilerFlag)
include(CheckIncludeFileCXX)
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict -std=c++11")
endif()
option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)

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doc/src/Eqs/fix_bond_react.tex Normal file
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@ -0,0 +1,9 @@
\documentstyle[12pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}
\end{eqnarray*}
\end{document}

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doc/src/PDF/pair_gayberne_extra.tex
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@ -48,8 +48,8 @@ $$ \mathbf{G}_{12} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
\mathbf{G}_2. $$
Let the relative energy matrices $\mathbf{E}_i = \mbox{diag}
(\epsilon_{ia}, \epsilon_{ib}, \epsilon_{ic})$ be given by
the relative well depths (dimensionless energy scales
(\epsilon_{ia}^{-1/\mu}, \epsilon_{ib}^{-1/\mu}, \epsilon_{ic}^{-1/\mu})$
be given by the relative well depths (dimensionless energy scales
inversely proportional to the well-depths of the respective
orthogonal configurations of the interacting molecules). The
$\chi$ orientation-dependent energy based on the user-specified
@ -62,8 +62,8 @@ $$ \hat{\mathbf{r}}_{12} = { \mathbf{r}_{12} } / |\mathbf{r}_{12}|, $$
and
$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1^2 \mathbf{A}_1 +
\mathbf{A}_2^T \mathbf{E}_2^2 \mathbf{A}_2 = \mathbf{B}_1 +
$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 +
\mathbf{A}_2^T \mathbf{E}_2 \mathbf{A}_2 = \mathbf{B}_1 +
\mathbf{B}_2. $$
Here, we use the distance of closest approach approximation given by the

25
doc/src/fix_bond_react.txt
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@ -266,7 +266,7 @@ either 'none' or 'charges.' Further details are provided in the
discussion of the 'update_edges' keyword. The fourth optional section
begins with the keyword 'Constraints' and lists additional criteria
that must be satisfied in order for the reaction to occur. Currently,
there are two types of constraints available, as discussed below.
there are three types of constraints available, as discussed below.
A sample map file is given below:
@ -320,6 +320,27 @@ the central atom). Angles must be specified in degrees. This
constraint can be used to enforce a certain orientation between
reacting molecules.
The constraint of type 'arrhenius' imposes an additional reaction
probability according to the temperature-dependent Arrhenius equation:
:c,image(Eqs/fix_bond_react.jpg)
The Arrhenius constraint has the following syntax:
arrhenius {A} {n} {E_a} {seed} :pre
where 'arrhenius' is the required keyword, {A} is the pre-exponential
factor, {n} is the exponent of the temperature dependence, {E_a} is
the activation energy ("units"_units.html of energy), and {seed} is a
random number seed. The temperature is defined as the instantaneous
temperature averaged over all atoms in the reaction site, and is
calculated in the same manner as for example
"compute_temp_chunk"_compute_temp_chunk.html. Currently, there are no
options for additional temperature averaging or velocity-biased
temperature calculations. A uniform random number between 0 and 1 is
generated using {seed}; if this number is less than the result of the
Arrhenius equation above, the reaction is permitted to occur.
Once a reaction site has been successfully identified, data structures
within LAMMPS that store bond topology are updated to reflect the
post-reacted molecule template. All force fields with fixed bonds,
@ -395,7 +416,7 @@ will apply to all reactions.
Computationally, each timestep this fix operates, it loops over
neighbor lists (for bond-forming reactions) and computes distances
between pairs of atoms in the list. It also communicates between
neighboring processors to coordinate which bonds are created and/or
neighboring processors to coordinate which bonds are created and/or
removed. All of these operations increase the cost of a timestep. Thus
you should be cautious about invoking this fix too frequently.

9
doc/src/pair_oxdna.txt
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@ -23,7 +23,7 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs
style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
args = list of arguments for these particular styles :ul
{oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
{oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
xi = temperature-independent coefficient in stacking strength
@ -36,7 +36,7 @@ args = list of arguments for these particular styles :ul
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -51,7 +51,10 @@ excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacki
and coaxial stacking interaction {oxdna/coaxstk} as well
as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
are supported "(Sulc)"_#Sulc1.
are supported "(Sulc)"_#Sulc1. Quasi-unique base-pairing between nucleotides can be achieved by using
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
up and down along the backbone.
The exact functional form of the pair styles is rather complex.
The individual potentials consist of products of modulation factors,

9
doc/src/pair_oxdna2.txt
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@ -24,7 +24,7 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/
style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
args = list of arguments for these particular styles :ul
{oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
{oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
xi = temperature-independent coefficient in stacking strength
@ -41,7 +41,7 @@ args = list of arguments for these particular styles :ul
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -57,7 +57,10 @@ excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stac
and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
are supported "(Sulc)"_#Sulc2.
are supported "(Sulc)"_#Sulc2. Quasi-unique base-pairing between nucleotides can be achieved by using
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
up and down along the backbone.
The exact functional form of the pair styles is rather complex.
The individual potentials consist of products of modulation factors,

1
doc/utils/sphinx-config/false_positives.txt
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@ -109,6 +109,7 @@ Archlinux
arcsin
arg
args
arrhenius
Arun
arXiv
asin

2
examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1
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@ -31,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

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examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2
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@ -31,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

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examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1
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@ -24,14 +24,14 @@ set atom * mass 3.1575
group all type 1 4
# oxDNA bond interactions - FENE backbone
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

34
examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 → examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.1
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@ -1,4 +1,4 @@
LAMMPS (18 Jun 2019)
LAMMPS (7 Aug 2019)
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
@ -35,8 +35,8 @@ read_data data.duplex1
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.000102 secs
read_data CPU = 0.002436 secs
special bonds CPU = 0.000116 secs
read_data CPU = 0.002026 secs
set atom * mass 3.1575
10 settings made for mass
@ -44,15 +44,15 @@ set atom * mass 3.1575
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -135,7 +135,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
999000 ekin = 0.190992053959174 | erot = 0.320462575795008 | epot = -15.1289686644104 | etot = -14.6175140346562
1000000 ekin = 0.179708146665509 | erot = 0.311553394429298 | epot = -15.1087755756885 | etot = -14.6175140345937
1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05
Loop time of 20.4903 on 1 procs for 1000000 steps with 10 atoms
Loop time of 18.4193 on 1 procs for 1000000 steps with 10 atoms
Performance: 42166.322 tau/day, 48803.614 timesteps/s
98.3% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 46907.305 tau/day, 54290.862 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 | 16.542 | 16.542 | 16.542 | 0.0 | 80.73
Bond | 0.62224 | 0.62224 | 0.62224 | 0.0 | 3.04
Pair | 14.935 | 14.935 | 14.935 | 0.0 | 81.08
Bond | 0.55556 | 0.55556 | 0.55556 | 0.0 | 3.02
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.21974 | 0.21974 | 0.21974 | 0.0 | 1.07
Comm | 0.16028 | 0.16028 | 0.16028 | 0.0 | 0.87
Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00
Modify | 2.7798 | 2.7798 | 2.7798 | 0.0 | 13.57
Other | | 0.3269 | | | 1.60
Modify | 2.5402 | 2.5402 | 2.5402 | 0.0 | 13.79
Other | | 0.2285 | | | 1.24
Nlocal: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -1169,4 +1169,4 @@ Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:20
Total wall time: 0:00:18

36
examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 → examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.4
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@ -1,4 +1,4 @@
LAMMPS (18 Jun 2019)
LAMMPS (7 Aug 2019)
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
@ -35,8 +35,8 @@ read_data data.duplex1
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.000196 secs
read_data CPU = 0.003266 secs
special bonds CPU = 0.000198 secs
read_data CPU = 0.004522 secs
set atom * mass 3.1575
10 settings made for mass
@ -44,15 +44,15 @@ set atom * mass 3.1575
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -135,7 +135,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
999000 ekin = 0.190992053959209 | erot = 0.320462575794744 | epot = -15.1289686644103 | etot = -14.6175140346563
1000000 ekin = 0.179708146665587 | erot = 0.311553394428757 | epot = -15.1087755756882 | etot = -14.6175140345938
1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05
Loop time of 28.9854 on 4 procs for 1000000 steps with 10 atoms
Loop time of 20.7945 on 4 procs for 1000000 steps with 10 atoms
Performance: 29808.075 tau/day, 34500.086 timesteps/s
96.6% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 41549.361 tau/day, 48089.538 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.85571 | 9.8341 | 18.111 | 228.8 | 33.93
Bond | 0.12393 | 0.38078 | 0.62324 | 32.7 | 1.31
Pair | 0.66725 | 7.9254 | 14.304 | 209.9 | 38.11
Bond | 0.095496 | 0.30973 | 0.49863 | 30.5 | 1.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.795 | 3.6269 | 4.4228 | 30.4 | 12.51
Output | 1.8e-05 | 2.575e-05 | 2.9e-05 | 0.0 | 0.00
Modify | 0.24721 | 1.1083 | 1.9206 | 64.1 | 3.82
Other | | 14.04 | | | 48.42
Comm | 1.8943 | 2.1825 | 2.4604 | 15.6 | 10.50
Output | 2e-05 | 2.9e-05 | 3.2e-05 | 0.0 | 0.00
Modify | 0.18231 | 0.95644 | 1.673 | 62.4 | 4.60
Other | | 9.421 | | | 45.30
Nlocal: 2.5 ave 5 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
@ -1169,4 +1169,4 @@ Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:28
Total wall time: 0:00:20

7
examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2
View File

@ -2,6 +2,7 @@ variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
units lj
dimension 3
@ -23,14 +24,14 @@ set atom * mass 3.1575
group all type 1 4
# oxDNA bond interactions - FENE backbone
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

37
examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 → examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.1
View File

@ -1,8 +1,9 @@
LAMMPS (18 Jun 2019)
LAMMPS (7 Aug 2019)
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
units lj
dimension 3
@ -34,8 +35,8 @@ read_data data.duplex2
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000103 secs
read_data CPU = 0.00215 secs
special bonds CPU = 0.000127 secs
read_data CPU = 0.001506 secs
set atom * mass 3.1575
16 settings made for mass
@ -43,15 +44,15 @@ set atom * mass 3.1575
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -136,7 +137,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.026 | 3.026 | 3.026 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
@ -1140,21 +1141,21 @@ Step Temp E_pair E_mol TotEng Press
999000 ekin = 2.08919327368179 | erot = 2.76364485800616 | epot = -20.9705413117635 | etot = -16.1177031800756
1000000 ekin = 2.11761701334905 | erot = 2.1409630347026 | epot = -20.9096627221725 | etot = -16.6510826741208
1000000 0.094116312 -1.3659956 0.059141691 -1.1745029 -3.0654283e-05
Loop time of 43.6978 on 1 procs for 1000000 steps with 16 atoms
Loop time of 39.73 on 1 procs for 1000000 steps with 16 atoms
Performance: 19772.150 tau/day, 22884.433 timesteps/s
98.6% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 21746.777 tau/day, 25169.881 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 32.769 | 32.769 | 32.769 | 0.0 | 74.99
Bond | 0.93071 | 0.93071 | 0.93071 | 0.0 | 2.13
Pair | 29.698 | 29.698 | 29.698 | 0.0 | 74.75
Bond | 0.84677 | 0.84677 | 0.84677 | 0.0 | 2.13
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.19584 | 0.19584 | 0.19584 | 0.0 | 0.45
Output | 1e-05 | 1e-05 | 1e-05 | 0.0 | 0.00
Modify | 9.4507 | 9.4507 | 9.4507 | 0.0 | 21.63
Other | | 0.3515 | | | 0.80
Comm | 0.15576 | 0.15576 | 0.15576 | 0.0 | 0.39
Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00
Modify | 8.7714 | 8.7714 | 8.7714 | 0.0 | 22.08
Other | | 0.2585 | | | 0.65
Nlocal: 16 ave 16 max 16 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -1170,4 +1171,4 @@ Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:43
Total wall time: 0:00:39

37
examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 → examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.4
View File

@ -1,8 +1,9 @@
LAMMPS (18 Jun 2019)
LAMMPS (7 Aug 2019)
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
units lj
dimension 3
@ -34,8 +35,8 @@ read_data data.duplex2
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000162 secs
read_data CPU = 0.002971 secs
special bonds CPU = 0.000188 secs
read_data CPU = 0.002335 secs
set atom * mass 3.1575
16 settings made for mass
@ -43,15 +44,15 @@ set atom * mass 3.1575
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -136,7 +137,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.778 | 7.96 | 8.143 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
@ -1140,21 +1141,21 @@ Step Temp E_pair E_mol TotEng Press
999000 ekin = 2.61553981530106 | erot = 1.7387289184571 | epot = -21.0217257279766 | etot = -16.6674569942185
1000000 ekin = 2.34012577497833 | erot = 2.86436388995813 | epot = -21.0201566044041 | etot = -15.8156669394676
1000000 0.10400559 -1.3746133 0.060853481 -1.1675019 0.00013752759
Loop time of 59.4195 on 4 procs for 1000000 steps with 16 atoms
Loop time of 44.9291 on 4 procs for 1000000 steps with 16 atoms
Performance: 14540.686 tau/day, 16829.497 timesteps/s
96.3% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 19230.287 tau/day, 22257.276 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0304 | 20.212 | 37.839 | 369.5 | 34.02
Bond | 0.12844 | 0.57006 | 0.95643 | 49.6 | 0.96
Pair | 0.75183 | 16.839 | 31.47 | 339.4 | 37.48
Bond | 0.10416 | 0.48181 | 0.82289 | 46.2 | 1.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 4.3935 | 5.5635 | 6.7052 | 44.2 | 9.36
Output | 2.3e-05 | 3.575e-05 | 4.1e-05 | 0.0 | 0.00
Modify | 0.3513 | 3.4695 | 6.4366 | 144.3 | 5.84
Other | | 29.6 | | | 49.82
Comm | 3.0032 | 3.0414 | 3.0759 | 1.7 | 6.77
Output | 1.6e-05 | 2.2e-05 | 2.4e-05 | 0.0 | 0.00
Modify | 0.25426 | 2.929 | 5.4956 | 134.9 | 6.52
Other | | 21.64 | | | 48.16
Nlocal: 4 ave 8 max 0 min
Histogram: 1 1 0 0 0 0 0 0 1 1
@ -1170,4 +1171,4 @@ Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:59
Total wall time: 0:00:44

6
examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
View File

@ -24,14 +24,14 @@ set atom * mass 1.0
group all type 1 4
# oxDNA bond interactions - FENE backbone
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

36
examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 → examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (18 Jun 2019)
LAMMPS (7 Aug 2019)
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
@ -35,8 +35,8 @@ read_data data.duplex3
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.000113 secs
read_data CPU = 0.00275 secs
special bonds CPU = 0.000145 secs
read_data CPU = 0.001965 secs
set atom * mass 1.0
10 settings made for mass
@ -44,15 +44,15 @@ set atom * mass 1.0
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -135,7 +135,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06
1000 ekin = 0.00366431201929618 | erot = 0.00193726360267488 | epot = -14.630505317301 | etot = -14.624903741679
@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
999000 ekin = 0.330110494517114 | erot = 0.658973630822449 | epot = -15.6139878677246 | etot = -14.624903742385
1000000 ekin = 0.345190458650495 | erot = 0.661138339466907 | epot = -15.6312325406154 | etot = -14.624903742498
1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06
Loop time of 20.5464 on 1 procs for 1000000 steps with 10 atoms
Loop time of 25.9663 on 1 procs for 1000000 steps with 10 atoms
Performance: 42051.215 tau/day, 48670.388 timesteps/s
98.3% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 33273.840 tau/day, 38511.388 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.716 | 16.716 | 16.716 | 0.0 | 81.36
Bond | 0.6285 | 0.6285 | 0.6285 | 0.0 | 3.06
Pair | 21.428 | 21.428 | 21.428 | 0.0 | 82.52
Bond | 0.76981 | 0.76981 | 0.76981 | 0.0 | 2.96
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.187 | 0.187 | 0.187 | 0.0 | 0.91
Output | 6e-06 | 6e-06 | 6e-06 | 0.0 | 0.00
Modify | 2.7186 | 2.7186 | 2.7186 | 0.0 | 13.23
Other | | 0.2965 | | | 1.44
Comm | 0.25709 | 0.25709 | 0.25709 | 0.0 | 0.99
Output | 9e-06 | 9e-06 | 9e-06 | 0.0 | 0.00
Modify | 3.1584 | 3.1584 | 3.1584 | 0.0 | 12.16
Other | | 0.3534 | | | 1.36
Nlocal: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -1169,4 +1169,4 @@ Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:20
Total wall time: 0:00:25

36
examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 → examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (18 Jun 2019)
LAMMPS (7 Aug 2019)
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
@ -35,8 +35,8 @@ read_data data.duplex3
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.000189 secs
read_data CPU = 0.003302 secs
special bonds CPU = 0.000188 secs
read_data CPU = 0.002791 secs
set atom * mass 1.0
10 settings made for mass
@ -44,15 +44,15 @@ set atom * mass 1.0
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -135,7 +135,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06
1000 ekin = 0.00366431201929595 | erot = 0.00193726360268106 | epot = -14.630505317301 | etot = -14.624903741679
@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
999000 ekin = 0.330110494517446 | erot = 0.658973630822486 | epot = -15.613987867725 | etot = -14.6249037423851
1000000 ekin = 0.345190458651126 | erot = 0.66113833946702 | epot = -15.6312325406162 | etot = -14.624903742498
1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06
Loop time of 30.1999 on 4 procs for 1000000 steps with 10 atoms
Loop time of 20.0167 on 4 procs for 1000000 steps with 10 atoms
Performance: 28609.339 tau/day, 33112.661 timesteps/s
96.4% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 43164.007 tau/day, 49958.342 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 | 0.90762 | 10.291 | 18.476 | 234.3 | 34.08
Bond | 0.11783 | 0.39332 | 0.61914 | 34.0 | 1.30
Pair | 0.59089 | 7.5652 | 13.908 | 205.5 | 37.79
Bond | 0.090803 | 0.29363 | 0.47758 | 29.6 | 1.47
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.8711 | 3.8042 | 4.7159 | 34.0 | 12.60
Output | 2e-05 | 3.15e-05 | 3.6e-05 | 0.0 | 0.00
Modify | 0.27052 | 1.1583 | 1.9428 | 63.9 | 3.84
Other | | 14.55 | | | 48.19
Comm | 1.7298 | 2.0312 | 2.2983 | 16.6 | 10.15
Output | 1.4e-05 | 2.075e-05 | 2.3e-05 | 0.0 | 0.00
Modify | 0.17638 | 0.90613 | 1.5893 | 60.1 | 4.53
Other | | 9.22 | | | 46.06
Nlocal: 2.5 ave 5 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
@ -1169,4 +1169,4 @@ Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:30
Total wall time: 0:00:20

25
src/ASPHERE/pair_gayberne.cpp
View File

@ -28,6 +28,7 @@
#include "citeme.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -460,20 +461,20 @@ void PairGayBerne::read_restart(FILE *fp)
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
if (me == 0) fread(&setwell[i],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setwell[i],1,MPI_INT,0,world);
if (setwell[i]) {
if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,NULL,error);
MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
}
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -505,12 +506,12 @@ void PairGayBerne::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&gamma,sizeof(double),1,fp);
fread(&upsilon,sizeof(double),1,fp);
fread(&mu,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&gamma,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&upsilon,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&gamma,1,MPI_DOUBLE,0,world);
MPI_Bcast(&upsilon,1,MPI_DOUBLE,0,world);

17
src/ASPHERE/pair_resquared.cpp
View File

@ -27,6 +27,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -438,20 +439,20 @@ void PairRESquared::read_restart(FILE *fp)
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
if (me == 0) fread(&setwell[i],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setwell[i],1,MPI_INT,0,world);
if (setwell[i]) {
if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,NULL,error);
MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
}
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -479,8 +480,8 @@ void PairRESquared::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);

23
src/CLASS2/angle_class2.cpp
View File

@ -27,6 +27,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -372,19 +373,19 @@ void AngleClass2::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
fread(&k2[1],sizeof(double),atom->nangletypes,fp);
fread(&k3[1],sizeof(double),atom->nangletypes,fp);
fread(&k4[1],sizeof(double),atom->nangletypes,fp);
utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&k3[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&k4[1],sizeof(double),atom->nangletypes,fp,NULL,error);
fread(&bb_k[1],sizeof(double),atom->nangletypes,fp);
fread(&bb_r1[1],sizeof(double),atom->nangletypes,fp);
fread(&bb_r2[1],sizeof(double),atom->nangletypes,fp);
utils::sfread(FLERR,&bb_k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&bb_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&bb_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
fread(&ba_k1[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_k2[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_r1[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_r2[1],sizeof(double),atom->nangletypes,fp);
utils::sfread(FLERR,&ba_k1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&ba_k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&ba_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&ba_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
}
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);

9
src/CLASS2/bond_class2.cpp
View File

@ -24,6 +24,7 @@
#include "force.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -182,10 +183,10 @@ void BondClass2::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
fread(&k2[1],sizeof(double),atom->nbondtypes,fp);
fread(&k3[1],sizeof(double),atom->nbondtypes,fp);
fread(&k4[1],sizeof(double),atom->nbondtypes,fp);
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&k2[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&k3[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&k4[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
}
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world);

65
src/CLASS2/dihedral_class2.cpp
View File

@ -27,6 +27,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -835,45 +836,45 @@ void DihedralClass2::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&k1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&k2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&k3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&phi1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&phi2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&phi3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
fread(&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
fread(&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
fread(&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
fread(&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
fread(&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
fread(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&aat_k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
fread(&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
}
MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

17
src/CLASS2/improper_class2.cpp
View File

@ -27,6 +27,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -604,15 +605,15 @@ void ImproperClass2::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k0[1],sizeof(double),atom->nimpropertypes,fp);
fread(&chi0[1],sizeof(double),atom->nimpropertypes,fp);
utils::sfread(FLERR,&k0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&chi0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
fread(&aa_k1[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_k2[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_k3[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_theta0_1[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_theta0_2[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_theta0_3[1],sizeof(double),atom->nimpropertypes,fp);
utils::sfread(FLERR,&aa_k1[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&aa_k2[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&aa_k3[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&aa_theta0_1[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&aa_theta0_2[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&aa_theta0_3[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
}
MPI_Bcast(&k0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&chi0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);

17
src/CLASS2/pair_lj_class2.cpp
View File

@ -24,6 +24,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -610,13 +611,13 @@ void PairLJClass2::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -645,10 +646,10 @@ void PairLJClass2::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);

21
src/CLASS2/pair_lj_class2_coul_cut.cpp
View File

@ -23,6 +23,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -362,14 +363,14 @@ void PairLJClass2CoulCut::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -399,11 +400,11 @@ void PairLJClass2CoulCut::write_restart_settings(FILE *fp)
void PairLJClass2CoulCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);

23
src/CLASS2/pair_lj_class2_coul_long.cpp
View File

@ -27,6 +27,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -805,13 +806,13 @@ void PairLJClass2CoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -842,13 +843,13 @@ void PairLJClass2CoulLong::write_restart_settings(FILE *fp)
void PairLJClass2CoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);

29
src/COLLOID/pair_brownian.cpp
View File

@ -36,6 +36,7 @@
#include "math_special.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -602,12 +603,12 @@ void PairBrownian::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&cut_inner[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@ -642,17 +643,17 @@ void PairBrownian::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&mu,sizeof(double),1,fp);
fread(&flaglog,sizeof(int),1,fp);
fread(&flagfld,sizeof(int),1,fp);
fread(&cut_inner_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&t_target, sizeof(double),1,fp);
fread(&seed, sizeof(int),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&flagHI,sizeof(int),1,fp);
fread(&flagVF,sizeof(int),1,fp);
utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&flaglog,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&flagfld,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&t_target, sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&seed, sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&flagHI,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&flagVF,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
MPI_Bcast(&flaglog,1,MPI_INT,0,world);

19
src/COLLOID/pair_colloid.cpp
View File

@ -25,6 +25,7 @@
#include "math_special.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathSpecial;
@ -394,15 +395,15 @@ void PairColloid::read_restart(FILE *fp)
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (comm->me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (comm->me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (comm->me == 0) {
fread(&a12[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&d1[i][j],sizeof(double),1,fp);
fread(&d2[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&a12[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&d1[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&d2[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&a12[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -432,9 +433,9 @@ void PairColloid::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);

25
src/COLLOID/pair_lubricate.cpp
View File

@ -35,6 +35,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -682,12 +683,12 @@ void PairLubricate::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&cut_inner[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@ -720,15 +721,15 @@ void PairLubricate::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&mu,sizeof(double),1,fp);
fread(&flaglog,sizeof(int),1,fp);
fread(&flagfld,sizeof(int),1,fp);
fread(&cut_inner_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&flagHI,sizeof(int),1,fp);
fread(&flagVF,sizeof(int),1,fp);
utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&flaglog,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&flagfld,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&flagHI,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&flagVF,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
MPI_Bcast(&flaglog,1,MPI_INT,0,world);

23
src/COLLOID/pair_lubricateU.cpp
View File

@ -34,6 +34,7 @@
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -1908,12 +1909,12 @@ void PairLubricateU::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&cut_inner[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@ -1945,14 +1946,14 @@ void PairLubricateU::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&mu,sizeof(double),1,fp);
fread(&flaglog,sizeof(int),1,fp);
fread(&cut_inner_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&flagHI,sizeof(int),1,fp);
fread(&flagVF,sizeof(int),1,fp);
utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&flaglog,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&flagHI,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&flagVF,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
MPI_Bcast(&flaglog,1,MPI_INT,0,world);

19
src/DIPOLE/pair_lj_cut_dipole_cut.cpp
View File

@ -23,6 +23,7 @@
#include "memory.h"
#include "error.h"
#include "update.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -437,14 +438,14 @@ void PairLJCutDipoleCut::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -473,10 +474,10 @@ void PairLJCutDipoleCut::write_restart_settings(FILE *fp)
void PairLJCutDipoleCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);

18
src/DIPOLE/pair_lj_cut_dipole_long.cpp
View File

@ -25,7 +25,7 @@
#include "memory.h"
#include "error.h"
#include "update.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -490,13 +490,13 @@ void PairLJCutDipoleLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -524,10 +524,10 @@ void PairLJCutDipoleLong::write_restart_settings(FILE *fp)
void PairLJCutDipoleLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);

19
src/DIPOLE/pair_lj_long_dipole_long.cpp
View File

@ -30,6 +30,7 @@
#include "update.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -344,13 +345,13 @@ void PairLJLongDipoleLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon_read[i][j],sizeof(double),1,fp);
fread(&sigma_read[i][j],sizeof(double),1,fp);
fread(&cut_lj_read[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon_read[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma_read[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj_read[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon_read[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_read[i][j],1,MPI_DOUBLE,0,world);
@ -379,11 +380,11 @@ void PairLJLongDipoleLong::write_restart_settings(FILE *fp)
void PairLJLongDipoleLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&ewald_order,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);

15
src/GRANULAR/pair_gran_hooke_history.cpp
View File

@ -31,6 +31,7 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -540,7 +541,7 @@ void PairGranHookeHistory::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
}
}
@ -566,12 +567,12 @@ void PairGranHookeHistory::write_restart_settings(FILE *fp)
void PairGranHookeHistory::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&kn,sizeof(double),1,fp);
fread(&kt,sizeof(double),1,fp);
fread(&gamman,sizeof(double),1,fp);
fread(&gammat,sizeof(double),1,fp);
fread(&xmu,sizeof(double),1,fp);
fread(&dampflag,sizeof(int),1,fp);
utils::sfread(FLERR,&kn,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&kt,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&gamman,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&gammat,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&xmu,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&dampflag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&kn,1,MPI_DOUBLE,0,world);
MPI_Bcast(&kt,1,MPI_DOUBLE,0,world);

23
src/GRANULAR/pair_granular.cpp
View File

@ -34,6 +34,7 @@ See the README file in the top-level LAMMPS directory.
#include "error.h"
#include "math_const.h"
#include "math_special.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -1251,20 +1252,20 @@ void PairGranular::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&normal_model[i][j],sizeof(int),1,fp);
fread(&damping_model[i][j],sizeof(int),1,fp);
fread(&tangential_model[i][j],sizeof(int),1,fp);
fread(&roll_model[i][j],sizeof(int),1,fp);
fread(&twist_model[i][j],sizeof(int),1,fp);
fread(normal_coeffs[i][j],sizeof(double),4,fp);
fread(tangential_coeffs[i][j],sizeof(double),3,fp);
fread(roll_coeffs[i][j],sizeof(double),3,fp);
fread(twist_coeffs[i][j],sizeof(double),3,fp);
fread(&cutoff_type[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&normal_model[i][j],sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&damping_model[i][j],sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tangential_model[i][j],sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&roll_model[i][j],sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&twist_model[i][j],sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,normal_coeffs[i][j],sizeof(double),4,fp,NULL,error);
utils::sfread(FLERR,tangential_coeffs[i][j],sizeof(double),3,fp,NULL,error);
utils::sfread(FLERR,roll_coeffs[i][j],sizeof(double),3,fp,NULL,error);
utils::sfread(FLERR,twist_coeffs[i][j],sizeof(double),3,fp,NULL,error);
utils::sfread(FLERR,&cutoff_type[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&normal_model[i][j],1,MPI_INT,0,world);
MPI_Bcast(&damping_model[i][j],1,MPI_INT,0,world);

1
src/KSPACE/fix_tune_kspace.cpp
View File

@ -29,6 +29,7 @@
#include "neighbor.h"
#include "modify.h"
#include "compute.h"
#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
#define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
#define GOLD 1.618034

29
src/KSPACE/pair_born_coul_long.cpp
View File

@ -27,6 +27,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -421,16 +422,16 @@ void PairBornCoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&a[i][j],sizeof(double),1,fp);
fread(&rho[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&c[i][j],sizeof(double),1,fp);
fread(&d[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&d[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@ -464,13 +465,13 @@ void PairBornCoulLong::write_restart_settings(FILE *fp)
void PairBornCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);

25
src/KSPACE/pair_buck_coul_long.cpp
View File

@ -24,6 +24,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -399,14 +400,14 @@ void PairBuckCoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&a[i][j],sizeof(double),1,fp);
fread(&rho[i][j],sizeof(double),1,fp);
fread(&c[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@ -438,13 +439,13 @@ void PairBuckCoulLong::write_restart_settings(FILE *fp)
void PairBuckCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);

25
src/KSPACE/pair_buck_long_coul_long.cpp
View File

@ -31,6 +31,7 @@
#include "respa.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -355,14 +356,14 @@ void PairBuckLongCoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&buck_a_read[i][j],sizeof(double),1,fp);
fread(&buck_rho_read[i][j],sizeof(double),1,fp);
fread(&buck_c_read[i][j],sizeof(double),1,fp);
fread(&cut_buck_read[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&buck_a_read[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&buck_rho_read[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&buck_c_read[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_buck_read[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&buck_a_read[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&buck_rho_read[i][j],1,MPI_DOUBLE,0,world);
@ -394,13 +395,13 @@ void PairBuckLongCoulLong::write_restart_settings(FILE *fp)
void PairBuckLongCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_buck_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
fread(&ewald_order,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_buck_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_buck_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);

15
src/KSPACE/pair_coul_long.cpp
View File

@ -27,6 +27,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -289,10 +290,10 @@ void PairCoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) fread(&scale[i][j],sizeof(double),1,fp);
if (me == 0) utils::sfread(FLERR,&scale[i][j],sizeof(double),1,fp,NULL,error);
MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world);
}
}
@ -318,11 +319,11 @@ void PairCoulLong::write_restart_settings(FILE *fp)
void PairCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);

25
src/KSPACE/pair_lj_charmm_coul_long.cpp
View File

@ -29,6 +29,7 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -822,14 +823,14 @@ void PairLJCharmmCoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&eps14[i][j],sizeof(double),1,fp);
fread(&sigma14[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -861,13 +862,13 @@ void PairLJCharmmCoulLong::write_restart_settings(FILE *fp)
void PairLJCharmmCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_inner,sizeof(double),1,fp);
fread(&cut_lj,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);

25
src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
View File

@ -33,6 +33,7 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -889,14 +890,14 @@ void PairLJCharmmfswCoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&eps14[i][j],sizeof(double),1,fp);
fread(&sigma14[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -928,13 +929,13 @@ void PairLJCharmmfswCoulLong::write_restart_settings(FILE *fp)
void PairLJCharmmfswCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_inner,sizeof(double),1,fp);
fread(&cut_lj,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);

23
src/KSPACE/pair_lj_cut_coul_long.cpp
View File

@ -31,6 +31,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -793,13 +794,13 @@ void PairLJCutCoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -830,13 +831,13 @@ void PairLJCutCoulLong::write_restart_settings(FILE *fp)
void PairLJCutCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);

25
src/KSPACE/pair_lj_cut_tip4p_long.cpp
View File

@ -30,6 +30,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -528,19 +529,19 @@ void PairLJCutTIP4PLong::write_restart_settings(FILE *fp)
void PairLJCutTIP4PLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&typeO,sizeof(int),1,fp);
fread(&typeH,sizeof(int),1,fp);
fread(&typeB,sizeof(int),1,fp);
fread(&typeA,sizeof(int),1,fp);
fread(&qdist,sizeof(double),1,fp);
utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&typeO,1,MPI_INT,0,world);

23
src/KSPACE/pair_lj_long_coul_long.cpp
View File

@ -33,6 +33,7 @@
#include "respa.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -355,13 +356,13 @@ void PairLJLongCoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon_read[i][j],sizeof(double),1,fp);
fread(&sigma_read[i][j],sizeof(double),1,fp);
fread(&cut_lj_read[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon_read[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma_read[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj_read[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon_read[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_read[i][j],1,MPI_DOUBLE,0,world);
@ -392,13 +393,13 @@ void PairLJLongCoulLong::write_restart_settings(FILE *fp)
void PairLJLongCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
fread(&ewald_order,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);

23
src/KSPACE/pair_lj_long_tip4p_long.cpp
View File

@ -30,6 +30,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -1539,18 +1540,18 @@ void PairLJLongTIP4PLong::write_restart_settings(FILE *fp)
void PairLJLongTIP4PLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&typeO,sizeof(int),1,fp);
fread(&typeH,sizeof(int),1,fp);
fread(&typeB,sizeof(int),1,fp);
fread(&typeA,sizeof(int),1,fp);
fread(&qdist,sizeof(double),1,fp);
utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&typeO,1,MPI_INT,0,world);

11
src/KSPACE/pair_tip4p_long.cpp
View File

@ -30,6 +30,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -467,11 +468,11 @@ void PairTIP4PLong::read_restart_settings(FILE *fp)
PairCoulLong::read_restart_settings(fp);
if (comm->me == 0) {
fread(&typeO,sizeof(int),1,fp);
fread(&typeH,sizeof(int),1,fp);
fread(&typeB,sizeof(int),1,fp);
fread(&typeA,sizeof(int),1,fp);
fread(&qdist,sizeof(double),1,fp);
utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&typeO,1,MPI_INT,0,world);

4
src/MAKE/OPTIONS/Makefile.intel_coprocessor
View File

@ -6,7 +6,7 @@ SHELL = /bin/sh
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpiicpc
CC = mpiicpc -std=c++11
MIC_OPT = -qoffload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
CCFLAGS = -g -O3 -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \
-xHost -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT \
@ -14,7 +14,7 @@ CCFLAGS = -g -O3 -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpiicpc
LINK = mpiicpc -std=c++11
LINKFLAGS = -g -O3 -xHost -qopenmp -qoffload
LIB = -ltbbmalloc
SIZE = size

4
src/MAKE/OPTIONS/Makefile.intel_cpu
View File

@ -6,7 +6,7 @@ SHELL = /bin/sh
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpiicpc
CC = mpiicpc -std=c++11
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
-qopt-zmm-usage=high
CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
@ -15,7 +15,7 @@ CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpiicpc
LINK = mpiicpc -std=c++11
LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
SIZE = size

4
src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
View File

@ -6,7 +6,7 @@ SHELL = /bin/sh
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpiicpc
CC = mpiicpc -std=c++11
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
-qopt-zmm-usage=high
CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
@ -15,7 +15,7 @@ CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpiicpc
LINK = mpiicpc -std=c++11
LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
SIZE = size

4
src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
View File

@ -6,7 +6,7 @@ SHELL = /bin/sh
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpicxx -cxx=icc
CC = mpicxx -cxx=icc -std=c++11
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
-qopt-zmm-usage=high
CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
@ -15,7 +15,7 @@ CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpicxx -cxx=icc
LINK = mpicxx -cxx=icc -std=c++11
LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
SIZE = size

4
src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi
View File

@ -7,7 +7,7 @@ SHELL = /bin/sh
# specify flags and libraries needed for your compiler
export OMPI_CXX = icc
CC = mpicxx
CC = mpicxx -std=c++11
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
-qopt-zmm-usage=high
CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
@ -16,7 +16,7 @@ CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpicxx
LINK = mpicxx -std=c++11
LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
SIZE = size

4
src/MAKE/OPTIONS/Makefile.knl
View File

@ -6,7 +6,7 @@ SHELL = /bin/sh
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpiicpc
CC = mpiicpc -std=c++11
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
@ -14,7 +14,7 @@ CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpiicpc
LINK = mpiicpc -std=c++11
LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
SIZE = size

9
src/MANYBODY/pair_atm.cpp
View File

@ -27,6 +27,7 @@
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -310,10 +311,10 @@ void PairATM::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) for (k = j; k <= atom->ntypes; k++) {
if (me == 0) fread(&nu[i][j][k],sizeof(double),1,fp);
if (me == 0) utils::sfread(FLERR,&nu[i][j][k],sizeof(double),1,fp,NULL,error);
MPI_Bcast(&nu[i][j][k],1,MPI_DOUBLE,0,world);
}
}
@ -338,8 +339,8 @@ void PairATM::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&cut_triple,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_triple,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_triple,1,MPI_DOUBLE,0,world);

17
src/MC/pair_dsmc.cpp
View File

@ -27,6 +27,7 @@
#include "domain.h"
#include "update.h"
#include "random_mars.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -345,12 +346,12 @@ void PairDSMC::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@ -378,11 +379,11 @@ void PairDSMC::write_restart_settings(FILE *fp)
void PairDSMC::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&max_cell_size,sizeof(double),1,fp);
fread(&seed,sizeof(int),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&max_cell_size,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);

21
src/MISC/pair_nm_cut.cpp
View File

@ -26,6 +26,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -318,15 +319,15 @@ void PairNMCut::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&e0[i][j],sizeof(double),1,fp);
fread(&r0[i][j],sizeof(double),1,fp);
fread(&nn[i][j],sizeof(double),1,fp);
fread(&mm[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
@ -356,10 +357,10 @@ void PairNMCut::write_restart_settings(FILE *fp)
void PairNMCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);

25
src/MISC/pair_nm_cut_coul_cut.cpp
View File

@ -27,6 +27,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -369,16 +370,16 @@ void PairNMCutCoulCut::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&e0[i][j],sizeof(double),1,fp);
fread(&r0[i][j],sizeof(double),1,fp);
fread(&nn[i][j],sizeof(double),1,fp);
fread(&mm[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
@ -410,11 +411,11 @@ void PairNMCutCoulCut::write_restart_settings(FILE *fp)
void PairNMCutCoulCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);

27
src/MISC/pair_nm_cut_coul_long.cpp
View File

@ -28,6 +28,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -413,15 +414,15 @@ void PairNMCutCoulLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&e0[i][j],sizeof(double),1,fp);
fread(&r0[i][j],sizeof(double),1,fp);
fread(&nn[i][j],sizeof(double),1,fp);
fread(&mm[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
@ -454,13 +455,13 @@ void PairNMCutCoulLong::write_restart_settings(FILE *fp)
void PairNMCutCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);

9
src/MOLECULE/angle_charmm.cpp
View File

@ -26,6 +26,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -245,10 +246,10 @@ void AngleCharmm::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
fread(&k_ub[1],sizeof(double),atom->nangletypes,fp);
fread(&r_ub[1],sizeof(double),atom->nangletypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&k_ub[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&r_ub[1],sizeof(double),atom->nangletypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);

3
src/MOLECULE/angle_cosine.cpp
View File

@ -22,6 +22,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -193,7 +194,7 @@ void AngleCosine::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) fread(&k[1],sizeof(double),atom->nangletypes,fp);
if (comm->me == 0) utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;

7
src/MOLECULE/angle_cosine_periodic.cpp
View File

@ -27,6 +27,7 @@
#include "math_special.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -246,9 +247,9 @@ void AngleCosinePeriodic::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&b[1],sizeof(int),atom->nangletypes,fp);
fread(&multiplicity[1],sizeof(int),atom->nangletypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&b[1],sizeof(int),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->nangletypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);

5
src/MOLECULE/angle_cosine_squared.cpp
View File

@ -26,6 +26,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -215,8 +216,8 @@ void AngleCosineSquared::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);

5
src/MOLECULE/angle_harmonic.cpp
View File

@ -22,6 +22,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -215,8 +216,8 @@ void AngleHarmonic::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);

5
src/MOLECULE/angle_table.cpp
View File

@ -29,6 +29,7 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -309,8 +310,8 @@ void AngleTable::write_restart_settings(FILE *fp)
void AngleTable::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&tabstyle,sizeof(int),1,fp);
fread(&tablength,sizeof(int),1,fp);
utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
MPI_Bcast(&tablength,1,MPI_INT,0,world);

9
src/MOLECULE/bond_fene.cpp
View File

@ -21,6 +21,7 @@
#include "force.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -215,10 +216,10 @@ void BondFENE::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
fread(&sigma[1],sizeof(double),atom->nbondtypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&sigma[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);

11
src/MOLECULE/bond_fene_expand.cpp
View File

@ -21,6 +21,7 @@
#include "force.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -224,11 +225,11 @@ void BondFENEExpand::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
fread(&sigma[1],sizeof(double),atom->nbondtypes,fp);
fread(&shift[1],sizeof(double),atom->nbondtypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&sigma[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&shift[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);

5
src/MOLECULE/bond_gromos.cpp
View File

@ -24,6 +24,7 @@
#include "force.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -166,8 +167,8 @@ void BondGromos::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);

5
src/MOLECULE/bond_harmonic.cpp
View File

@ -21,6 +21,7 @@
#include "force.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -167,8 +168,8 @@ void BondHarmonic::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);

7
src/MOLECULE/bond_morse.cpp
View File

@ -24,6 +24,7 @@
#include "force.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -171,9 +172,9 @@ void BondMorse::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&d0[1],sizeof(double),atom->nbondtypes,fp);
fread(&alpha[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
utils::sfread(FLERR,&d0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&alpha[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
}
MPI_Bcast(&d0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[1],atom->nbondtypes,MPI_DOUBLE,0,world);

7
src/MOLECULE/bond_nonlinear.cpp
View File

@ -20,6 +20,7 @@
#include "force.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -166,9 +167,9 @@ void BondNonlinear::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
fread(&lamda[1],sizeof(double),atom->nbondtypes,fp);
utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&lamda[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
}
MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);

11
src/MOLECULE/bond_quartic.cpp
View File

@ -25,6 +25,7 @@
#include "pair.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -275,11 +276,11 @@ void BondQuartic::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&b1[1],sizeof(double),atom->nbondtypes,fp);
fread(&b2[1],sizeof(double),atom->nbondtypes,fp);
fread(&rc[1],sizeof(double),atom->nbondtypes,fp);
fread(&u0[1],sizeof(double),atom->nbondtypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&b1[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&b2[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&rc[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
utils::sfread(FLERR,&u0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&b1[1],atom->nbondtypes,MPI_DOUBLE,0,world);

4
src/MOLECULE/bond_table.cpp
View File

@ -252,8 +252,8 @@ void BondTable::write_restart_settings(FILE *fp)
void BondTable::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&tabstyle,sizeof(int),1,fp);
fread(&tablength,sizeof(int),1,fp);
utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
MPI_Bcast(&tablength,1,MPI_INT,0,world);

11
src/MOLECULE/dihedral_charmm.cpp
View File

@ -29,6 +29,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -423,11 +424,11 @@ void DihedralCharmm::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&weightflag,sizeof(int),1,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&shift[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&weight[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&weightflag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);

11
src/MOLECULE/dihedral_charmmfsw.cpp
View File

@ -32,6 +32,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -466,11 +467,11 @@ void DihedralCharmmfsw::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&weightflag,sizeof(int),1,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&shift[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&weight[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&weightflag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);

7
src/MOLECULE/dihedral_harmonic.cpp
View File

@ -25,6 +25,7 @@
#include "update.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -327,9 +328,9 @@ void DihedralHarmonic::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&sign[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&sign[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sign[1],atom->ndihedraltypes,MPI_INT,0,world);

7
src/MOLECULE/dihedral_helix.cpp
View File

@ -27,6 +27,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -322,9 +323,9 @@ void DihedralHelix::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&aphi[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bphi[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&cphi[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&aphi[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&bphi[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&cphi[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
}
MPI_Bcast(&aphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

11
src/MOLECULE/dihedral_multi_harmonic.cpp
View File

@ -25,6 +25,7 @@
#include "update.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -318,11 +319,11 @@ void DihedralMultiHarmonic::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&a1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&a2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&a3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&a4[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&a5[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&a1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&a2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&a3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&a4[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&a5[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
}
MPI_Bcast(&a1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&a2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

9
src/MOLECULE/dihedral_opls.cpp
View File

@ -25,6 +25,7 @@
#include "update.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -330,10 +331,10 @@ void DihedralOPLS::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k4[1],sizeof(double),atom->ndihedraltypes,fp);
utils::sfread(FLERR,&k1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&k2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&k3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
utils::sfread(FLERR,&k4[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
}
MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

7
src/MOLECULE/improper_cvff.cpp
View File

@ -21,6 +21,7 @@
#include "update.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -333,9 +334,9 @@ void ImproperCvff::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
fread(&sign[1],sizeof(int),atom->nimpropertypes,fp);
fread(&multiplicity[1],sizeof(int),atom->nimpropertypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&sign[1],sizeof(int),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->nimpropertypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sign[1],atom->nimpropertypes,MPI_INT,0,world);

5
src/MOLECULE/improper_harmonic.cpp
View File

@ -22,6 +22,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -274,8 +275,8 @@ void ImproperHarmonic::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
}
MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);

7
src/MOLECULE/improper_umbrella.cpp
View File

@ -26,6 +26,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -315,9 +316,9 @@ void ImproperUmbrella::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
fread(&kw[1],sizeof(double),atom->nimpropertypes,fp);
fread(&w0[1],sizeof(double),atom->nimpropertypes,fp);
fread(&C[1],sizeof(double),atom->nimpropertypes,fp);
utils::sfread(FLERR,&kw[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&w0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
utils::sfread(FLERR,&C[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
}
MPI_Bcast(&kw[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&w0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);

23
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
View File

@ -26,6 +26,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -374,14 +375,14 @@ void PairLJCharmmCoulCharmm::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&eps14[i][j],sizeof(double),1,fp);
fread(&sigma14[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -435,12 +436,12 @@ void PairLJCharmmCoulCharmm::write_restart_settings(FILE *fp)
void PairLJCharmmCoulCharmm::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_inner,sizeof(double),1,fp);
fread(&cut_lj,sizeof(double),1,fp);
fread(&cut_coul_inner,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul_inner,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);

21
src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
View File

@ -31,6 +31,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -432,14 +433,14 @@ void PairLJCharmmfswCoulCharmmfsh::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&eps14[i][j],sizeof(double),1,fp);
fread(&sigma14[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -469,11 +470,11 @@ void PairLJCharmmfswCoulCharmmfsh::write_restart_settings(FILE *fp)
void PairLJCharmmfswCoulCharmmfsh::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_inner,sizeof(double),1,fp);
fread(&cut_lj,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);

29
src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
View File

@ -30,6 +30,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -617,13 +618,13 @@ void PairLJCutTIP4PCut::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -659,17 +660,17 @@ void PairLJCutTIP4PCut::write_restart_settings(FILE *fp)
void PairLJCutTIP4PCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&typeO,sizeof(int),1,fp);
fread(&typeH,sizeof(int),1,fp);
fread(&typeB,sizeof(int),1,fp);
fread(&typeA,sizeof(int),1,fp);
fread(&qdist,sizeof(double),1,fp);
utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&typeO,1,MPI_INT,0,world);

15
src/MOLECULE/pair_tip4p_cut.cpp
View File

@ -28,6 +28,7 @@
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -474,7 +475,7 @@ void PairTIP4PCut::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
}
}
@ -501,13 +502,13 @@ void PairTIP4PCut::write_restart_settings(FILE *fp)
void PairTIP4PCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&typeO,sizeof(int),1,fp);
fread(&typeH,sizeof(int),1,fp);
fread(&typeB,sizeof(int),1,fp);
fread(&typeA,sizeof(int),1,fp);
fread(&qdist,sizeof(double),1,fp);
utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
fread(&cut_coul,sizeof(double),1,fp);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&typeO,1,MPI_INT,0,world);

15
src/PERI/pair_peri_eps.cpp
View File

@ -31,6 +31,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -564,16 +565,16 @@ void PairPeriEPS::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&bulkmodulus[i][j],sizeof(double),1,fp);
fread(&shearmodulus[i][j],sizeof(double),1,fp);
fread(&s00[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
fread(&m_yieldstress[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&bulkmodulus[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&shearmodulus[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&m_yieldstress[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);

13
src/PERI/pair_peri_lps.cpp
View File

@ -31,6 +31,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "math_const.h"
using namespace LAMMPS_NS;
@ -489,15 +490,15 @@ void PairPeriLPS::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&bulkmodulus[i][j],sizeof(double),1,fp);
fread(&shearmodulus[i][j],sizeof(double),1,fp);
fread(&s00[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&bulkmodulus[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&shearmodulus[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);

11
src/PERI/pair_peri_pmb.cpp
View File

@ -32,6 +32,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -418,14 +419,14 @@ void PairPeriPMB::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&kspring[i][j],sizeof(double),1,fp);
fread(&s00[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&kspring[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&kspring[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);

17
src/PERI/pair_peri_ves.cpp
View File

@ -31,6 +31,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "update.h"
using namespace LAMMPS_NS;
@ -547,17 +548,17 @@ void PairPeriVES::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&bulkmodulus[i][j],sizeof(double),1,fp);
fread(&shearmodulus[i][j],sizeof(double),1,fp);
fread(&s00[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
fread(&m_lambdai[i][j],sizeof(double),1,fp);
fread(&m_taubi[i][j],sizeof(double),1,fp);
utils::sfread(FLERR,&bulkmodulus[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&shearmodulus[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&m_lambdai[i][j],sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&m_taubi[i][j],sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);

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