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Marco De Lucia
RedModRphree
Commits
be82c72c
Commit
be82c72c
authored
3 years ago
by
Marco De Lucia
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MDL: some fixes for CRAN submission
parent
7673975e
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!2
Bumped to 0.3.3; fixed AddProp, removed all references to "ListInfo",...
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R/Rphree_ReactTrans.R
+38
-34
38 additions, 34 deletions
R/Rphree_ReactTrans.R
R/Rphree_SurrogateUtils.R
+2
-3
2 additions, 3 deletions
R/Rphree_SurrogateUtils.R
with
40 additions
and
37 deletions
R/Rphree_ReactTrans.R
+
38
−
34
View file @
be82c72c
## Functions for dealing with surrogate simulations
## Functions for dealing with surrogate simulations
### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
### Time-stamp: "Last modified 2021-04-28 15:
30
:4
7
delucia"
### Time-stamp: "Last modified 2021-04-28 15:
54
:4
8
delucia"
##' Todo
##' This function takes the current state of a chemical system in form
##' of a matrix, a vector of concentrations representing boundary
##' conditions (injection), the required time step (dt/s), grid spcing
##' (dx/m) and U (Darcy velocity/m^3/s). Note that it is
##' responsibility of user to check that the required dt does not
##' trespass the CFL condition.
##'
##'
##' @title Simple explicit 1D forward-Euler advection, multispecies
##' @title Simple explicit 1D forward-Euler advection, multispecies
##' @param conc matrix containing the chemical state
##' @param conc either a vector or a matrix containing the chemical
##' state to be updated
##' @param inflow vector of concentrations entering the inlet
##' @param inflow vector of concentrations entering the inlet
##' @param dx the grid spacing in m
##' @param dx the grid spacing in m
##' @param dt the required time step in s
##' @param dt the required time step in s
##' @param U
Darcy velocity in m^3/s
##' @param U Darcy velocity in m^3/s
##' @return a matrix containing the state after the advection
##' @return a matrix containing the state after the advection
##' @author MDL
##' @author MDL
##' @export
##' @export
AdvectionPQC
<-
function
(
conc
,
inflow
=
rep
(
0
,
ncol
(
conc
)),
dx
,
dt
,
U
)
AdvectionPQC
<-
function
(
conc
,
inflow
=
rep
(
0
,
ncol
(
conc
)),
dx
,
dt
,
U
)
{
{
if
(
is.matrix
(
conc
))
{
if
(
is.matrix
(
conc
))
{
## msg("conc is matrix")
## CurrConc <<- conc
## actually the first iteration does not have the attributes attached
## actually the first iteration does not have the attributes attached
if
(
"immobile"
%in%
names
(
attributes
(
conc
))
)
{
if
(
"immobile"
%in%
names
(
attributes
(
conc
))
)
{
immobile
<-
attr
(
conc
,
"immobile"
)
immobile
<-
attr
(
conc
,
"immobile"
)
...
@@ -146,8 +150,6 @@ Act2pH <- function(state){
...
@@ -146,8 +150,6 @@ Act2pH <- function(state){
}
}
##' TODO
##'
##' @title Recompose a chemical state after reduction
##' @title Recompose a chemical state after reduction
##' @param state the state to be recomposed
##' @param state the state to be recomposed
##' @param reduced the initial reduced state containing the "index" attribute
##' @param reduced the initial reduced state containing the "index" attribute
...
@@ -168,13 +170,13 @@ RecomposeState <- function(state, reduced)
...
@@ -168,13 +170,13 @@ RecomposeState <- function(state, reduced)
return
(
res
)
return
(
res
)
}
}
##' This functions requires the package \code{mgcv}
##' Applies \code{mgcv::uniquecombs} to the matrix representing the
##'
##' current chemical state.
##' TODO
##' @title Finds unique problems in a geochemical state
##' @title Finds unique problems in a geochemical state
##' @param data the matrix
##' @param data the matrix
##' @return a matrix plus an attribute containing the indeces of the
##' @return a matrix with attached attribute containing the indeces of
##' compressed matrix
##' the compressed matrix for later restoring and the "immobile"
##' indices
##' @author MDL
##' @author MDL
##' @export
##' @export
ReduceState
<-
function
(
data
)
ReduceState
<-
function
(
data
)
...
@@ -187,7 +189,7 @@ ReduceState <- function(data)
...
@@ -187,7 +189,7 @@ ReduceState <- function(data)
##'
TODO
##'
Cfr \code{demo}
##' @title 1D Reactive transport simulations using phreeqc or a
##' @title 1D Reactive transport simulations using phreeqc or a
##' surrogate, equilibrium simulations
##' surrogate, equilibrium simulations
##' @param setup a list with several input parameters
##' @param setup a list with several input parameters
...
@@ -291,11 +293,12 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
...
@@ -291,11 +293,12 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
pad
<-
floor
(
log10
(
maxiter
+1
))
+1
## to properly format the step names
pad
<-
floor
(
log10
(
maxiter
+1
))
+1
## to properly format the step names
spr_string
<-
paste0
(
"%0"
,
pad
,
"d"
)
spr_string
<-
paste0
(
"%0"
,
pad
,
"d"
)
names
(
saved_complete
)
<-
paste0
(
"step_"
,
sprintf
(
spr_string
,
seq
(
0
,
maxiter
)))
names
(
saved_complete
)
<-
paste0
(
"step_"
,
sprintf
(
spr_string
,
seq
(
0
,
maxiter
)))
out_inp
<<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
utils
::
globalVariables
(
c
(
"out_inp"
,
"out_res"
,
"out_bal"
))
out_res
<<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_bal
<<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_inp
<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_of_tol
<<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_res
<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_bal
<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
timing
<-
matrix
(
NA
,
ncol
=
5
,
nrow
=
maxiter
)
timing
<-
matrix
(
NA
,
ncol
=
5
,
nrow
=
maxiter
)
...
@@ -332,7 +335,6 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
...
@@ -332,7 +335,6 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
attr
(
state_C
,
"immobile"
)
<-
immobile
attr
(
state_C
,
"immobile"
)
<-
immobile
## ssC <<- state_C
index_saved
<-
1
index_saved
<-
1
saved_complete
[[
index_saved
]]
<-
list
(
C
=
Act2pH
(
state_C
))
saved_complete
[[
index_saved
]]
<-
list
(
C
=
Act2pH
(
state_C
))
index_saved
<-
index_saved
+
1
index_saved
<-
index_saved
+
1
...
@@ -372,8 +374,8 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
...
@@ -372,8 +374,8 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
saved_complete
[[
index_saved
]]
<-
list
(
T
=
Act2pH
(
state_T
),
C
=
Act2pH
(
state_C
))
saved_complete
[[
index_saved
]]
<-
list
(
T
=
Act2pH
(
state_T
),
C
=
Act2pH
(
state_C
))
index_saved
<-
index_saved
+
1
index_saved
<-
index_saved
+
1
out_inp
[[
1
]]
<
<-
inplist
out_inp
[[
1
]]
<-
inplist
out_res
[[
1
]]
<
<-
res_C
out_res
[[
1
]]
<-
res_C
if
(
ebreak
)
{
if
(
ebreak
)
{
msg
(
"Early break invoked, bye."
)
msg
(
"Early break invoked, bye."
)
...
@@ -426,7 +428,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
...
@@ -426,7 +428,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
Tm
<-
system.time
(
tmpsur
<-
Selected.Surrogate
(
reduced
,
model
=
model
)
)[
3
]
Tm
<-
system.time
(
tmpsur
<-
Selected.Surrogate
(
reduced
,
model
=
model
)
)[
3
]
bal
<-
CheckBalance
(
baleq
,
reduced
,
tmpsur
)
bal
<-
CheckBalance
(
baleq
,
reduced
,
tmpsur
)
out_bal
[[
iter
]]
<
<-
bal
out_bal
[[
iter
]]
<-
bal
totbal
<-
apply
(
bal
,
1
,
mae
)
totbal
<-
apply
(
bal
,
1
,
mae
)
nonok
<-
which
(
totbal
>
tol
)
### max(tol,tol2))
nonok
<-
which
(
totbal
>
tol
)
### max(tol,tol2))
...
@@ -455,7 +457,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
...
@@ -455,7 +457,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
## new input
## new input
Ts
<-
system.time
(
inplist
<-
splitMultiFix
(
data
=
reduced
,
procs
=
procs
,
base
=
base
,
first
=
first
,
Ts
<-
system.time
(
inplist
<-
splitMultiFix
(
data
=
reduced
,
procs
=
procs
,
base
=
base
,
first
=
first
,
prop
=
prop
,
minerals
=
immobile
,
nmax
=
maxsim
))[
3
]
prop
=
prop
,
minerals
=
immobile
,
nmax
=
maxsim
))[
3
]
out_inp
[[
iter
]]
<
<-
inplist
out_inp
[[
iter
]]
<-
inplist
Tm
<-
system.time
(
res_C
<-
RunPQC
(
inplist
,
procs
=
procs
))[
3
]
Tm
<-
system.time
(
res_C
<-
RunPQC
(
inplist
,
procs
=
procs
))[
3
]
attr
(
res_C
,
"immobile"
)
<-
immobile
attr
(
res_C
,
"immobile"
)
<-
immobile
}
}
...
@@ -473,7 +475,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
...
@@ -473,7 +475,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
## ## transform the pH/pe back into activities
## ## transform the pH/pe back into activities
## state_C <- pH2Act(state_C)
## state_C <- pH2Act(state_C)
out_res
[[
iter
]]
<
<-
res_C
out_res
[[
iter
]]
<-
res_C
timing
[
iter
,]
<-
c
(
dim
(
reduced
)[
1
],
procs
,
Tm
,
Tr
,
Ts
)
timing
[
iter
,]
<-
c
(
dim
(
reduced
)[
1
],
procs
,
Tm
,
Tr
,
Ts
)
msg
(
"done iteration"
,
iter
,
"/"
,
maxiter
,
" CPU-time "
,
round
(
Tm
,
3
),
"[s]"
)
msg
(
"done iteration"
,
iter
,
"/"
,
maxiter
,
" CPU-time "
,
round
(
Tm
,
3
),
"[s]"
)
...
@@ -601,10 +603,12 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
...
@@ -601,10 +603,12 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
pad
<-
floor
(
log10
(
maxiter
+1
))
+1
## to properly format the step names
pad
<-
floor
(
log10
(
maxiter
+1
))
+1
## to properly format the step names
spr_string
<-
paste0
(
"%0"
,
pad
,
"d"
)
spr_string
<-
paste0
(
"%0"
,
pad
,
"d"
)
names
(
saved_complete
)
<-
paste0
(
"step_"
,
sprintf
(
spr_string
,
seq
(
0
,
maxiter
)))
names
(
saved_complete
)
<-
paste0
(
"step_"
,
sprintf
(
spr_string
,
seq
(
0
,
maxiter
)))
utils
::
globalVariables
(
c
(
"out_inp"
,
"out_res"
,
"out_bal"
))
out_inp
<
<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_inp
<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_res
<
<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_res
<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_bal
<
<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
out_bal
<-
vector
(
mode
=
"list"
,
length
=
length
(
maxiter
))
timing
<-
matrix
(
NA
,
ncol
=
5
,
nrow
=
maxiter
)
timing
<-
matrix
(
NA
,
ncol
=
5
,
nrow
=
maxiter
)
msg
(
"Loading phreeqc db... "
)
msg
(
"Loading phreeqc db... "
)
...
@@ -675,8 +679,8 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
...
@@ -675,8 +679,8 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
saved_complete
[[
index_saved
]]
<-
list
(
T
=
Act2pH
(
state_T
),
C
=
Act2pH
(
state_C
))
saved_complete
[[
index_saved
]]
<-
list
(
T
=
Act2pH
(
state_T
),
C
=
Act2pH
(
state_C
))
index_saved
<-
index_saved
+
1
index_saved
<-
index_saved
+
1
out_inp
[[
1
]]
<
<-
inplist
out_inp
[[
1
]]
<-
inplist
out_res
[[
1
]]
<
<-
res_C
out_res
[[
1
]]
<-
res_C
if
(
ebreak
)
{
if
(
ebreak
)
{
msg
(
"Early break invoked, bye."
)
msg
(
"Early break invoked, bye."
)
...
@@ -730,7 +734,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
...
@@ -730,7 +734,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
Tm
<-
system.time
(
tmpsur
<-
Selected.Surrogate
(
reduced
,
model
=
model
)
)[
3
]
Tm
<-
system.time
(
tmpsur
<-
Selected.Surrogate
(
reduced
,
model
=
model
)
)[
3
]
## print(head(tmpsur))
## print(head(tmpsur))
bal
<-
CheckBalance
(
baleq
,
reduced
,
tmpsur
)
bal
<-
CheckBalance
(
baleq
,
reduced
,
tmpsur
)
out_bal
[[
iter
]]
<
<-
bal
out_bal
[[
iter
]]
<-
bal
totbal
<-
apply
(
bal
,
1
,
mae
)
totbal
<-
apply
(
bal
,
1
,
mae
)
## cat(":: Surrogate Balance Summary:\n")
## cat(":: Surrogate Balance Summary:\n")
...
@@ -747,7 +751,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
...
@@ -747,7 +751,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
Ts
<-
Ts
+
system.time
(
inplist
<-
splitMultiKin
(
data
=
reducednonok
,
procs
=
procs
,
base
=
base
,
first
=
first
,
ann
=
ann
,
Ts
<-
Ts
+
system.time
(
inplist
<-
splitMultiKin
(
data
=
reducednonok
,
procs
=
procs
,
base
=
base
,
first
=
first
,
ann
=
ann
,
prop
=
prop
,
minerals
=
immobile
,
kin
=
kin
,
dt
=
dt
,
nmax
=
maxsim
))[
3
]
prop
=
prop
,
minerals
=
immobile
,
kin
=
kin
,
dt
=
dt
,
nmax
=
maxsim
))[
3
]
out_inp
[[
iter
]]
<
<-
inplist
out_inp
[[
iter
]]
<-
inplist
if
(
length
(
nonok
)
==
1
)
{
if
(
length
(
nonok
)
==
1
)
{
Tm
<-
Tm
+
system.time
(
tmp2
<-
RunPQC
(
inplist
,
procs
=
1
))[
3
]
Tm
<-
Tm
+
system.time
(
tmp2
<-
RunPQC
(
inplist
,
procs
=
1
))[
3
]
pqcres_C
<-
tmp2
[,
prop
]
pqcres_C
<-
tmp2
[,
prop
]
...
@@ -765,7 +769,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
...
@@ -765,7 +769,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
## new input
## new input
Ts
<-
system.time
(
inplist
<-
splitMultiKin
(
data
=
reduced
,
procs
=
procs
,
base
=
base
,
first
=
first
,
ann
=
ann
,
Ts
<-
system.time
(
inplist
<-
splitMultiKin
(
data
=
reduced
,
procs
=
procs
,
base
=
base
,
first
=
first
,
ann
=
ann
,
prop
=
prop
,
minerals
=
immobile
,
kin
=
kin
,
dt
=
dt
,
nmax
=
maxsim
))[
3
]
prop
=
prop
,
minerals
=
immobile
,
kin
=
kin
,
dt
=
dt
,
nmax
=
maxsim
))[
3
]
out_inp
[[
iter
]]
<
<-
inplist
out_inp
[[
iter
]]
<-
inplist
Tm
<-
system.time
(
tmp3
<-
RunPQC
(
inplist
,
procs
=
procs
))[
3
]
Tm
<-
system.time
(
tmp3
<-
RunPQC
(
inplist
,
procs
=
procs
))[
3
]
res_C
<-
tmp3
[,
prop
]
res_C
<-
tmp3
[,
prop
]
attr
(
res_C
,
"immobile"
)
<-
immobile
attr
(
res_C
,
"immobile"
)
<-
immobile
...
@@ -784,7 +788,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
...
@@ -784,7 +788,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
## transform the pH/pe back into activities
## transform the pH/pe back into activities
state_C
<-
pH2Act
(
state_C
)
state_C
<-
pH2Act
(
state_C
)
out_res
[[
iter
]]
<
<-
res_C
out_res
[[
iter
]]
<-
res_C
timing
[
iter
,]
<-
c
(
dim
(
reduced
)[
1
],
procs
,
Tm
,
Tr
,
Ts
)
timing
[
iter
,]
<-
c
(
dim
(
reduced
)[
1
],
procs
,
Tm
,
Tr
,
Ts
)
msg
(
"done iteration"
,
iter
,
"/"
,
maxiter
,
" CPU-time "
,
round
(
Tm
,
3
),
"[s]"
)
msg
(
"done iteration"
,
iter
,
"/"
,
maxiter
,
" CPU-time "
,
round
(
Tm
,
3
),
"[s]"
)
...
...
This diff is collapsed.
Click to expand it.
R/Rphree_SurrogateUtils.R
+
2
−
3
View file @
be82c72c
## Functions for dealing with surrogate simulations
## Functions for dealing with surrogate simulations
### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
### Time-stamp: "Last modified 2021-04-28 15:
32:05
delucia"
### Time-stamp: "Last modified 2021-04-28 15:
44:10
delucia"
##' Computes the average of absolute values of a vector
##' Computes the average of absolute values of a vector
##' @title Average of absolute values
##' @title Average of absolute values
...
@@ -94,9 +94,8 @@ ExtractSpecies <- function(flatlist, species) {
...
@@ -94,9 +94,8 @@ ExtractSpecies <- function(flatlist, species) {
##' @param flatlist the list as input to search in
##' @param flatlist the list as input to search in
##' @param pphases character vector containing the names of the Pure
##' @param pphases character vector containing the names of the Pure
##' Phases whose values are to be extracted
##' Phases whose values are to be extracted
##' @param species vector containing the names of the species to
##' search for
##' @return a matrix containing as many columns as specified pphases
##' @return a matrix containing as many columns as specified pphases
##' @export
##' @author MDL
##' @author MDL
ExtractPphases
<-
function
(
flatlist
,
pphases
)
{
ExtractPphases
<-
function
(
flatlist
,
pphases
)
{
tmp
<-
matrix
(
NA
,
len
<-
length
(
flatlist
),
speclen
<-
length
(
pphases
))
tmp
<-
matrix
(
NA
,
len
<-
length
(
flatlist
),
speclen
<-
length
(
pphases
))
...
...
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