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Tony's latest changes.

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New test case SC_Ohm, added to Makefile.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10983 1feff8c3-07ed-0310-ac33-dd36852eb9cd
This commit is contained in:
David L Parkhurst 2016-03-26 20:11:29 +00:00
parent d5e7aa0ab3
commit d2dba8c291
3 changed files with 179 additions and 147 deletions
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1
Phreeqc.h
View File

@ -1408,6 +1408,7 @@ protected:
int multi_Dflag; /* signals calc'n of multicomponent diffusion */ int multi_Dflag; /* signals calc'n of multicomponent diffusion */
int interlayer_Dflag; /* multicomponent diffusion and diffusion through interlayer porosity */ int interlayer_Dflag; /* multicomponent diffusion and diffusion through interlayer porosity */
LDBLE default_Dw; /* default species diffusion coefficient in water at 25oC, m2/s */ LDBLE default_Dw; /* default species diffusion coefficient in water at 25oC, m2/s */
int correct_Dw; /* if true, Dw is adapted in calc_SC */
LDBLE multi_Dpor; /* uniform porosity of free porewater in solid medium */ LDBLE multi_Dpor; /* uniform porosity of free porewater in solid medium */
LDBLE interlayer_Dpor; /* uniform porosity of interlayer space of montmorillonite in solid medium */ LDBLE interlayer_Dpor; /* uniform porosity of interlayer space of montmorillonite in solid medium */
LDBLE multi_Dpor_lim; /* limiting free porewater porosity where transport stops */ LDBLE multi_Dpor_lim; /* limiting free porewater porosity where transport stops */

303
readtr.cpp
View File

@ -21,19 +21,19 @@ int Phreeqc::
read_transport(void) read_transport(void)
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
{ {
/* /*
* Reads advection and column information * Reads advection and column information
* *
* Arguments: * Arguments:
* none * none
* *
* Returns: * Returns:
* KEYWORD if keyword encountered, input_error may be incremented if * KEYWORD if keyword encountered, input_error may be incremented if
* a keyword is encountered in an unexpected position * a keyword is encountered in an unexpected position
* EOF if eof encountered while reading mass balance concentrations * EOF if eof encountered while reading mass balance concentrations
* ERROR if error occurred reading data * ERROR if error occurred reading data
* *
*/ */
char *ptr; char *ptr;
int i, j, l; int i, j, l;
int count_length, count_disp, count_punch, count_print, count_por; int count_length, count_disp, count_punch, count_print, count_por;
@ -96,9 +96,9 @@ read_transport(void)
int count_opt_list = 44; int count_opt_list = 44;
strcpy(file_name, "phreeqc.dmp"); strcpy(file_name, "phreeqc.dmp");
/* /*
* Initialize * Initialize
*/ */
simul_tr++; simul_tr++;
if (simul_tr == 1) if (simul_tr == 1)
{ {
@ -111,7 +111,7 @@ read_transport(void)
old_cells = count_cells; old_cells = count_cells;
count_length = count_disp = count_punch = count_print = count_por = 0; count_length = count_disp = count_punch = count_print = count_por = 0;
length = (LDBLE *) PHRQ_malloc(sizeof(LDBLE)); length = (LDBLE *)PHRQ_malloc(sizeof(LDBLE));
if (length == NULL) if (length == NULL)
malloc_error(); malloc_error();
@ -127,25 +127,25 @@ read_transport(void)
if (punch_temp == NULL) if (punch_temp == NULL)
malloc_error(); malloc_error();
print_temp = (int *) PHRQ_malloc(sizeof(int)); print_temp = (int *)PHRQ_malloc(sizeof(int));
if (print_temp == NULL) if (print_temp == NULL)
malloc_error(); malloc_error();
count_length_alloc = count_disp_alloc = count_por_alloc = 1; count_length_alloc = count_disp_alloc = count_por_alloc = 1;
transport_start = 1; transport_start = 1;
/* /*
* Read transport number (not currently used) * Read transport number (not currently used)
*/ */
ptr = line; ptr = line;
read_number_description(ptr, &n_user, &n_user_end, &description); read_number_description(ptr, &n_user, &n_user_end, &description);
description = (char *) free_check_null(description); description = (char *)free_check_null(description);
/* /*
* Set use data to last read * Set use data to last read
*/ */
use.Set_trans_in(true); use.Set_trans_in(true);
/* /*
* Read lines * Read lines
*/ */
opt_save = OPTION_DEFAULT; opt_save = OPTION_DEFAULT;
return_value = UNKNOWN; return_value = UNKNOWN;
for (;;) for (;;)
@ -190,7 +190,7 @@ read_transport(void)
input_error++; input_error++;
error_msg error_msg
("Expected shift direction, -1, 0, 1. Use -direction instead.", ("Expected shift direction, -1, 0, 1. Use -direction instead.",
CONTINUE); CONTINUE);
ishift = 1; ishift = 1;
} }
} }
@ -200,7 +200,7 @@ read_transport(void)
case 20: /* print_cells */ case 20: /* print_cells */
print_temp = print_temp =
read_list_ints_range(&next_char, &count_print, FALSE, read_list_ints_range(&next_char, &count_print, FALSE,
print_temp); print_temp);
opt_save = 2; opt_save = 2;
break; break;
case 3: /* selected_output */ case 3: /* selected_output */
@ -211,7 +211,7 @@ read_transport(void)
if (punch_modulus <= 0) if (punch_modulus <= 0)
{ {
error_string = sformatf( error_string = sformatf(
"Punch frequency must be greater than 0. Frequency set to 1000."); "Punch frequency must be greater than 0. Frequency set to 1000.");
warning_msg(error_string); warning_msg(error_string);
punch_modulus = 1000; punch_modulus = 1000;
} }
@ -231,7 +231,7 @@ read_transport(void)
input_error++; input_error++;
error_msg error_msg
("Expected boundary condition to be 'constant' (1), 'closed' (2) , or 'flux' (3).", ("Expected boundary condition to be 'constant' (1), 'closed' (2) , or 'flux' (3).",
CONTINUE); CONTINUE);
} }
} }
else if (i == EMPTY) else if (i == EMPTY)
@ -247,7 +247,7 @@ read_transport(void)
input_error++; input_error++;
error_msg error_msg
("Expected boundary condition to be 'constant', 'closed', or 'flux'.", ("Expected boundary condition to be 'constant', 'closed', or 'flux'.",
CONTINUE); CONTINUE);
} }
/* last cell boundary condition */ /* last cell boundary condition */
@ -261,7 +261,7 @@ read_transport(void)
input_error++; input_error++;
error_msg error_msg
("Expected boundary condition to be 'constant' (1), 'closed' (2) , or 'flux' (3).", ("Expected boundary condition to be 'constant' (1), 'closed' (2) , or 'flux' (3).",
CONTINUE); CONTINUE);
} }
} }
else if (i == EMPTY) else if (i == EMPTY)
@ -277,7 +277,7 @@ read_transport(void)
input_error++; input_error++;
error_msg error_msg
("Expected boundary condition to be 'constant', 'closed', or 'flux'.", ("Expected boundary condition to be 'constant', 'closed', or 'flux'.",
CONTINUE); CONTINUE);
} }
opt_save = OPTION_DEFAULT; opt_save = OPTION_DEFAULT;
break; break;
@ -304,7 +304,7 @@ read_transport(void)
{ {
mcd_substeps = 1.0; mcd_substeps = 1.0;
warning_msg("Substep factor in MCD must be >= 1.0\n" warning_msg("Substep factor in MCD must be >= 1.0\n"
"mcd_substeps = 1.0 assumed."); "mcd_substeps = 1.0 assumed.");
} }
opt_save = OPTION_DEFAULT; opt_save = OPTION_DEFAULT;
break; break;
@ -324,7 +324,7 @@ read_transport(void)
tempr = 1; tempr = 1;
warning_msg warning_msg
("Temperature retardation factor < 1 is not possible.\n" ("Temperature retardation factor < 1 is not possible.\n"
"Temperature retardation factor = 1 assumed."); "Temperature retardation factor = 1 assumed.");
} }
j = copy_token(token, &next_char, &l); j = copy_token(token, &next_char, &l);
if (j == DIGIT) if (j == DIGIT)
@ -335,11 +335,11 @@ read_transport(void)
case 24: /* lengths */ case 24: /* lengths */
if (read_line_LDBLEs if (read_line_LDBLEs
(next_char, &length, &count_length, (next_char, &length, &count_length,
&count_length_alloc) == ERROR) &count_length_alloc) == ERROR)
{ {
input_error++; input_error++;
error_msg("Reading lengths in TRANSPORT keyword.\n", error_msg("Reading lengths in TRANSPORT keyword.\n",
CONTINUE); CONTINUE);
} }
opt_save = 8; opt_save = 8;
break; break;
@ -351,7 +351,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_msg("Reading dispersivities in TRANSPORT keyword.\n", error_msg("Reading dispersivities in TRANSPORT keyword.\n",
CONTINUE); CONTINUE);
} }
opt_save = 9; opt_save = 9;
break; break;
@ -360,7 +360,7 @@ read_transport(void)
case 30: /* punch_cells */ case 30: /* punch_cells */
punch_temp = punch_temp =
read_list_ints_range(&next_char, &count_punch, FALSE, read_list_ints_range(&next_char, &count_punch, FALSE,
punch_temp); punch_temp);
opt_save = 10; opt_save = 10;
break; break;
case 11: /* stagnant */ case 11: /* stagnant */
@ -371,7 +371,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expecting number of stagnant layers."); "Expecting number of stagnant layers.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -384,7 +384,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expecting exchange factor for stagnant layers."); "Expecting exchange factor for stagnant layers.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -393,7 +393,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expecting porosity in the mobile zone."); "Expecting porosity in the mobile zone.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -402,7 +402,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expecting porosity in the immobile zone."); "Expecting porosity in the immobile zone.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -428,7 +428,7 @@ read_transport(void)
input_error++; input_error++;
error_msg error_msg
("Expected flow direction to be 'forward', 'back', or 'no_flow'.", ("Expected flow direction to be 'forward', 'back', or 'no_flow'.",
CONTINUE); CONTINUE);
} }
opt_save = OPTION_DEFAULT; opt_save = OPTION_DEFAULT;
break; break;
@ -452,7 +452,7 @@ read_transport(void)
if (print_modulus <= 0) if (print_modulus <= 0)
{ {
error_string = sformatf( error_string = sformatf(
"Print frequency must be greater than 0. Frequency set to 1000."); "Print frequency must be greater than 0. Frequency set to 1000.");
warning_msg(error_string); warning_msg(error_string);
print_modulus = 1000; print_modulus = 1000;
} }
@ -513,12 +513,13 @@ read_transport(void)
input_error++; input_error++;
error_msg error_msg
("Expected multicomponent diffusion flag: 'true' or 'false'.", ("Expected multicomponent diffusion flag: 'true' or 'false'.",
CONTINUE); CONTINUE);
} }
default_Dw = 1e-9; default_Dw = 1e-9;
multi_Dpor = 0.3; multi_Dpor = 0.3;
multi_Dpor_lim = 0.0; multi_Dpor_lim = 0.0;
multi_Dn = 1.0; multi_Dn = 1.0;
correct_Dw = 0;
if (copy_token(token, &next_char, &l) == EMPTY) if (copy_token(token, &next_char, &l) == EMPTY)
break; break;
else else
@ -528,7 +529,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expected default species diffusion coefficient in water at 25oC, m2/s."); "Expected default species diffusion coefficient in water at 25oC, m2/s.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -542,7 +543,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expected porosity to calculate diffusion coefficient."); "Expected porosity to calculate diffusion coefficient.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -556,7 +557,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expected porosity limit for diffusive transport."); "Expected porosity limit for diffusive transport.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -569,11 +570,28 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expected exponent for porosity reduction of diffusion coefficient (Dp = Dw * (por)^n)."); "Expected exponent for porosity reduction of diffusion coefficient (Dp = Dw * (por)^n).");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
} }
if (copy_token(token, &next_char, &l) == EMPTY)
break;
else
{
str_tolower(token);
if (strstr(token, "f") == token)
correct_Dw = 0;
else if (strstr(token, "t") == token)
correct_Dw = 1;
else
{
input_error++;
error_msg
("Expected 'true' or 'false' for correcting Dw's as in Specific Conductance.",
CONTINUE);
}
}
opt_save = OPTION_DEFAULT; opt_save = OPTION_DEFAULT;
break; break;
case 41: /* interlayer diffusion */ case 41: /* interlayer diffusion */
@ -588,7 +606,7 @@ read_transport(void)
input_error++; input_error++;
error_msg error_msg
("Expected interlayer diffusion flag: 'true' or 'false'.", ("Expected interlayer diffusion flag: 'true' or 'false'.",
CONTINUE); CONTINUE);
} }
interlayer_Dpor = 0.1; interlayer_Dpor = 0.1;
interlayer_Dpor_lim = 0.0; interlayer_Dpor_lim = 0.0;
@ -601,7 +619,7 @@ read_transport(void)
if (sscanf(token, SCANFORMAT, &interlayer_Dpor) != 1) if (sscanf(token, SCANFORMAT, &interlayer_Dpor) != 1)
{ {
input_error++; input_error++;
error_string = sformatf( "Expected interlayer porosity."); error_string = sformatf("Expected interlayer porosity.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -615,7 +633,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expected interlayer porosity limit for diffusive transport."); "Expected interlayer porosity limit for diffusive transport.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -628,7 +646,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Expected interlayer tortuosity factor (Dp = Dw /t_f)."); "Expected interlayer tortuosity factor (Dp = Dw /t_f).");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
break; break;
} }
@ -651,9 +669,9 @@ read_transport(void)
if (return_value == EOF || return_value == KEYWORD) if (return_value == EOF || return_value == KEYWORD)
break; break;
} }
/* /*
* Determine number of cells * Determine number of cells
*/ */
max_cells = count_cells; max_cells = count_cells;
if (count_length > max_cells) if (count_length > max_cells)
max_cells = count_length; max_cells = count_length;
@ -666,8 +684,8 @@ read_transport(void)
if (max_cells == count_length) if (max_cells == count_length)
{ {
sprintf(token, sprintf(token,
"Number of cells is increased to number of 'lengths' %d.", "Number of cells is increased to number of 'lengths' %d.",
count_length); count_length);
warning_msg(token); warning_msg(token);
} }
else if (max_cells == count_disp) else if (max_cells == count_disp)
@ -685,9 +703,9 @@ read_transport(void)
// warning_msg(token); // warning_msg(token);
//} //}
} }
/* /*
* Allocate space for cell_data * Allocate space for cell_data
*/ */
int all_cells_now = max_cells * (1 + stag_data->count_stag) + 2; int all_cells_now = max_cells * (1 + stag_data->count_stag) + 2;
space((void **)((void *)&cell_data), all_cells_now, &cell_data_max_cells, space((void **)((void *)&cell_data), all_cells_now, &cell_data_max_cells,
sizeof(struct cell_data)); sizeof(struct cell_data));
@ -701,7 +719,7 @@ read_transport(void)
cell_data[i].mid_cell_x = 1.0; cell_data[i].mid_cell_x = 1.0;
cell_data[i].disp = 1.0; cell_data[i].disp = 1.0;
cell_data[i].temp = 25.0; cell_data[i].temp = 25.0;
cell_data[i].por = 0.3; cell_data[i].por = 0.3;
cell_data[i].por_il = 0.01; cell_data[i].por_il = 0.01;
cell_data[i].potV = 0; cell_data[i].potV = 0;
cell_data[i].punch = FALSE; cell_data[i].punch = FALSE;
@ -710,15 +728,15 @@ read_transport(void)
all_cells = all_cells_now; all_cells = all_cells_now;
} }
/* /*
* Fill in data for lengths * Fill in data for lengths
*/ */
if (count_length == 0) if (count_length == 0)
{ {
if (old_cells < max_cells) if (old_cells < max_cells)
{ {
error_string = sformatf( error_string = sformatf(
"No cell-lengths were read; length = 1 m assumed."); "No cell-lengths were read; length = 1 m assumed.");
warning_msg(error_string); warning_msg(error_string);
for (i = 1; i <= max_cells; i++) for (i = 1; i <= max_cells; i++)
cell_data[i].length = 1.0; cell_data[i].length = 1.0;
@ -733,8 +751,8 @@ read_transport(void)
if (max_cells > count_length) if (max_cells > count_length)
{ {
error_string = sformatf( error_string = sformatf(
"Cell-lengths were read for %d cells. Last value is used till cell %d.", "Cell-lengths were read for %d cells. Last value is used till cell %d.",
count_length, max_cells); count_length, max_cells);
warning_msg(error_string); warning_msg(error_string);
for (i = count_length; i <= max_cells; i++) for (i = count_length; i <= max_cells; i++)
cell_data[i + 1].length = length[count_length - 1]; cell_data[i + 1].length = length[count_length - 1];
@ -749,9 +767,9 @@ read_transport(void)
} }
cell_data[max_cells + 1].mid_cell_x = cell_data[max_cells + 1].mid_cell_x =
cell_data[max_cells].mid_cell_x + cell_data[max_cells].length / 2; cell_data[max_cells].mid_cell_x + cell_data[max_cells].length / 2;
/* /*
* Fill in data for dispersivities * Fill in data for dispersivities
*/ */
if (count_disp == 0) if (count_disp == 0)
{ {
if (old_cells < max_cells) if (old_cells < max_cells)
@ -777,9 +795,9 @@ read_transport(void)
cell_data[i + 1].disp = disp[count_disp - 1]; cell_data[i + 1].disp = disp[count_disp - 1];
} }
} }
/* /*
* Fill in data for porosities * Fill in data for porosities
*/ */
if (count_por == 0) if (count_por == 0)
{ {
if (old_cells < all_cells && multi_Dflag) if (old_cells < all_cells && multi_Dflag)
@ -793,7 +811,6 @@ read_transport(void)
"No porosities were read; used the minimal value %8.2e from -multi_D.", multi_Dpor); "No porosities were read; used the minimal value %8.2e from -multi_D.", multi_Dpor);
warning_msg(error_string); warning_msg(error_string);
for (i = old_cells + 1; i < all_cells; i++) for (i = old_cells + 1; i < all_cells; i++)
//for (i = old_cells; i < all_cells; i++)
cell_data[i].por = multi_Dpor; cell_data[i].por = multi_Dpor;
} }
} }
@ -838,9 +855,9 @@ read_transport(void)
cell_data[i].por_il = interlayer_Dpor; cell_data[i].por_il = interlayer_Dpor;
} }
count_cells = max_cells; count_cells = max_cells;
/* /*
* Account for stagnant cells * Account for stagnant cells
*/ */
if (stag_data->count_stag > 0) if (stag_data->count_stag > 0)
{ {
max_cells = count_cells * (1 + stag_data->count_stag) + 2; max_cells = count_cells * (1 + stag_data->count_stag) + 2;
@ -848,12 +865,12 @@ read_transport(void)
{ {
for (l = 1; l <= stag_data->count_stag; l++) for (l = 1; l <= stag_data->count_stag; l++)
cell_data[i + 1 + l * count_cells].mid_cell_x = cell_data[i + 1 + l * count_cells].mid_cell_x =
cell_data[i].mid_cell_x; cell_data[i].mid_cell_x;
} }
} }
/* /*
* Fill in data for punch * Fill in data for punch
*/ */
if (count_punch != 0) if (count_punch != 0)
{ {
for (i = 0; i < all_cells; i++) for (i = 0; i < all_cells; i++)
@ -863,8 +880,8 @@ read_transport(void)
if (punch_temp[i] > all_cells - 1 || punch_temp[i] < 0) if (punch_temp[i] > all_cells - 1 || punch_temp[i] < 0)
{ {
error_string = sformatf( error_string = sformatf(
"Cell number for punch is out of range, %d. Request ignored.", "Cell number for punch is out of range, %d. Request ignored.",
punch_temp[i]); punch_temp[i]);
warning_msg(error_string); warning_msg(error_string);
} }
else else
@ -874,9 +891,9 @@ read_transport(void)
else if (simul_tr == 1) else if (simul_tr == 1)
for (i = 1; i < all_cells; i++) for (i = 1; i < all_cells; i++)
cell_data[i].punch = TRUE; cell_data[i].punch = TRUE;
/* /*
* Fill in data for print * Fill in data for print
*/ */
if (count_print != 0) if (count_print != 0)
{ {
for (i = 0; i < all_cells; i++) for (i = 0; i < all_cells; i++)
@ -886,8 +903,8 @@ read_transport(void)
if (print_temp[i] > all_cells - 1 || print_temp[i] < 0) if (print_temp[i] > all_cells - 1 || print_temp[i] < 0)
{ {
error_string = sformatf( error_string = sformatf(
"Cell number for print is out of range, %d. Request ignored.", "Cell number for print is out of range, %d. Request ignored.",
print_temp[i]); print_temp[i]);
warning_msg(error_string); warning_msg(error_string);
} }
else else
@ -899,7 +916,7 @@ read_transport(void)
cell_data[i].print = TRUE; cell_data[i].print = TRUE;
//#define OLD_POROSITY //#define OLD_POROSITY
#if defined(OLD_POROSITY) #if defined(OLD_POROSITY)
/* /*
* Fill in porosities * Fill in porosities
*/ */
if (interlayer_Dflag && !multi_Dflag) if (interlayer_Dflag && !multi_Dflag)
@ -929,8 +946,8 @@ read_transport(void)
//} //}
/* /*
* Calculate dump_modulus * Calculate dump_modulus
*/ */
if (dump_in == TRUE) if (dump_in == TRUE)
{ {
if (dump_modulus == 0) if (dump_modulus == 0)
@ -945,14 +962,14 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Starting shift for transport, %d, is greater than number of shifts, %d.", "Starting shift for transport, %d, is greater than number of shifts, %d.",
transport_start, count_shifts); transport_start, count_shifts);
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
} }
} }
/* /*
* Check boundary conditions * Check boundary conditions
*/ */
if ((ishift != 0) && ((bcon_first == 2) || (bcon_last == 2))) if ((ishift != 0) && ((bcon_first == 2) || (bcon_last == 2)))
{ {
warning_msg warning_msg
@ -962,17 +979,17 @@ read_transport(void)
if (bcon_last == 2) if (bcon_last == 2)
bcon_last = 3; bcon_last = 3;
} }
/* /*
* Retain data from previous run * Retain data from previous run
*/ */
if (simul_tr > 1) if (simul_tr > 1)
{ {
if ((count_length == 0) && (count_disp == 0) && (count_por == 0)) if ((count_length == 0) && (count_disp == 0) && (count_por == 0))
dup_print("Column data retained from former run", TRUE); dup_print("Column data retained from former run", TRUE);
} }
/* /*
* Check heat_diffc * Check heat_diffc
*/ */
if (heat_diffc < 0) if (heat_diffc < 0)
heat_diffc = diffc; heat_diffc = diffc;
else if (stag_data->count_stag == 1) else if (stag_data->count_stag == 1)
@ -983,14 +1000,14 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Must enter diffusion coefficient (-diffc) when modeling thermal diffusion."); "Must enter diffusion coefficient (-diffc) when modeling thermal diffusion.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
} }
else if (heat_diffc > diffc) else if (heat_diffc > diffc)
{ {
error_string = sformatf( error_string = sformatf(
"Thermal diffusion is calculated assuming exchange factor was for\n\t effective (non-thermal) diffusion coefficient = %e.", "Thermal diffusion is calculated assuming exchange factor was for\n\t effective (non-thermal) diffusion coefficient = %e.",
(double) diffc); (double)diffc);
warning_msg(error_string); warning_msg(error_string);
} }
} }
@ -1000,7 +1017,7 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Must enter value for mobile/stagnant exchange factor when modeling thermal diffusion."); "Must enter value for mobile/stagnant exchange factor when modeling thermal diffusion.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
} }
} }
@ -1009,17 +1026,17 @@ read_transport(void)
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
"Only one stagnant layer permitted (-stag) when modeling thermal diffusion."); "Only one stagnant layer permitted (-stag) when modeling thermal diffusion.");
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
} }
/* /*
* free storage for length, disp, punch * free storage for length, disp, punch
*/ */
length = (LDBLE *) free_check_null(length); length = (LDBLE *)free_check_null(length);
disp = (LDBLE *) free_check_null(disp); disp = (LDBLE *)free_check_null(disp);
pors = (LDBLE *) free_check_null(pors); pors = (LDBLE *)free_check_null(pors);
punch_temp = (int *) free_check_null(punch_temp); punch_temp = (int *)free_check_null(punch_temp);
print_temp = (int *) free_check_null(print_temp); print_temp = (int *)free_check_null(print_temp);
if (dump_in == TRUE) if (dump_in == TRUE)
{ {
@ -1079,9 +1096,9 @@ int Phreeqc::
dump_cpp(void) dump_cpp(void)
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
{ {
/* /*
* dumps solution compositions to file * dumps solution compositions to file
*/ */
int l; int l;
@ -1094,26 +1111,26 @@ dump_cpp(void)
std::ofstream fs(dump_file_name_cpp.c_str()); std::ofstream fs(dump_file_name_cpp.c_str());
if (!fs.is_open()) if (!fs.is_open())
{ {
error_string = sformatf( "Can`t open file, %s.", dump_file_name_cpp.c_str()); error_string = sformatf("Can`t open file, %s.", dump_file_name_cpp.c_str());
input_error++; input_error++;
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
return (OK); return (OK);
} }
fs << "# Dumpfile" << "\n" << "# Transport simulation " << simul_tr << " Shift " << transport_step << "\n" << "#" << "\n"; fs << "# Dumpfile" << "\n" << "# Transport simulation " << simul_tr << " Shift " << transport_step << "\n" << "#" << "\n";
phreeqcBin.dump_raw(fs, 0); phreeqcBin.dump_raw(fs, 0);
fs << "END" << "\n"; fs << "END" << "\n";
char token[MAX_LENGTH]; char token[MAX_LENGTH];
sprintf(token, "KNOBS\n"); sprintf(token, "KNOBS\n");
fs << token;
sprintf(token, "\t-iter%15d\n", itmax);
fs << token;
sprintf(token, "\t-tol %15.3e\n", (double) ineq_tol);
fs << token;
sprintf(token, "\t-step%15.3e\n", (double) step_size);
fs << token; fs << token;
sprintf(token, "\t-pe_s%15.3e\n", (double) pe_step_size); sprintf(token, "\t-iter%15d\n", itmax);
fs << token;
sprintf(token, "\t-tol %15.3e\n", (double)ineq_tol);
fs << token;
sprintf(token, "\t-step%15.3e\n", (double)step_size);
fs << token;
sprintf(token, "\t-pe_s%15.3e\n", (double)pe_step_size);
fs << token; fs << token;
sprintf(token, "\t-diag "); sprintf(token, "\t-diag ");
fs << token; fs << token;
@ -1128,12 +1145,12 @@ dump_cpp(void)
fs << token; fs << token;
} }
std::map < int, SelectedOutput >::iterator so_it = SelectedOutput_map.begin(); std::map < int, SelectedOutput >::iterator so_it = SelectedOutput_map.begin();
for ( ; so_it != SelectedOutput_map.end(); so_it++) for (; so_it != SelectedOutput_map.end(); so_it++)
{ {
current_selected_output = &(so_it->second); current_selected_output = &(so_it->second);
sprintf(token, "SELECTED_OUTPUT %d\n", current_selected_output->Get_n_user()); sprintf(token, "SELECTED_OUTPUT %d\n", current_selected_output->Get_n_user());
fs << token ; fs << token;
//sprintf(token, "\t-file %-15s\n", "sel_o$$$.prn"); //sprintf(token, "\t-file %-15s\n", "sel_o$$$.prn");
//fs << token; //fs << token;
fs << "\t-file " << "sel_o$$$" << current_selected_output->Get_n_user() << ".prn\n"; fs << "\t-file " << "sel_o$$$" << current_selected_output->Get_n_user() << ".prn\n";
@ -1248,19 +1265,19 @@ dump_cpp(void)
fs << token; fs << token;
sprintf(token, "\t-bcon %6d%6d\n", bcon_first, bcon_last); sprintf(token, "\t-bcon %6d%6d\n", bcon_first, bcon_last);
fs << token; fs << token;
sprintf(token, "\t-timest %13.5e\n", (double) timest); sprintf(token, "\t-timest %13.5e\n", (double)timest);
fs << token; fs << token;
if (!high_precision) if (!high_precision)
{ {
sprintf(token, "\t-diffc %13.5e\n", (double) diffc); sprintf(token, "\t-diffc %13.5e\n", (double)diffc);
fs << token; fs << token;
} }
else else
{ {
sprintf(token, "\t-diffc %20.12e\n", (double) diffc); sprintf(token, "\t-diffc %20.12e\n", (double)diffc);
fs << token; fs << token;
} }
sprintf(token, "\t-tempr %13.5e\n", (double) tempr); sprintf(token, "\t-tempr %13.5e\n", (double)tempr);
fs << token; fs << token;
if (correct_disp == TRUE) if (correct_disp == TRUE)
{ {
@ -1276,7 +1293,7 @@ dump_cpp(void)
fs << token; fs << token;
for (int i = 1; i <= count_cells; i++) for (int i = 1; i <= count_cells; i++)
{ {
sprintf(token, "%12.3e", (double) cell_data[i].length); sprintf(token, "%12.3e", (double)cell_data[i].length);
fs << token; fs << token;
if (i > 0 && (i % 8) == 0) if (i > 0 && (i % 8) == 0)
{ {
@ -1292,12 +1309,12 @@ dump_cpp(void)
{ {
if (!high_precision) if (!high_precision)
{ {
sprintf(token, "%12.3e", (double) cell_data[i].disp); sprintf(token, "%12.3e", (double)cell_data[i].disp);
fs << token; fs << token;
} }
else else
{ {
sprintf(token, "%20.12e", (double) cell_data[i].disp); sprintf(token, "%20.12e", (double)cell_data[i].disp);
fs << token; fs << token;
} }
if (i > 0 && (i % 8) == 0) if (i > 0 && (i % 8) == 0)
@ -1366,9 +1383,9 @@ int Phreeqc::
dump(void) dump(void)
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
{ {
/* /*
* dumps solution compositions to file * dumps solution compositions to file
*/ */
if (dump_in == FALSE || pr.dump == FALSE) if (dump_in == FALSE || pr.dump == FALSE)
return (OK); return (OK);

22
transport.cpp
View File

@ -527,7 +527,7 @@ transport(void)
run_reactions(i, kin_time, NOMIX, step_fraction); run_reactions(i, kin_time, NOMIX, step_fraction);
else else
run_reactions(i, kin_time, DISP, step_fraction); run_reactions(i, kin_time, DISP, step_fraction);
if (multi_Dflag && j < nmix) if (multi_Dflag)
fill_spec(i); fill_spec(i);
/* punch and output file */ /* punch and output file */
@ -707,7 +707,7 @@ transport(void)
transport_step, 0, i, max_iter); transport_step, 0, i, max_iter);
status(0, token); status(0, token);
run_reactions(i, kin_time, NOMIX, step_fraction); run_reactions(i, kin_time, NOMIX, step_fraction);
if (multi_Dflag == TRUE && j < nmix) if (multi_Dflag == TRUE)
fill_spec(i); fill_spec(i);
if (iterations > max_iter) if (iterations > max_iter)
max_iter = iterations; max_iter = iterations;
@ -825,7 +825,7 @@ transport(void)
run_reactions(i, kin_time, NOMIX, step_fraction); run_reactions(i, kin_time, NOMIX, step_fraction);
else else
run_reactions(i, kin_time, DISP, step_fraction); run_reactions(i, kin_time, DISP, step_fraction);
if (multi_Dflag == TRUE && j < nmix) if (multi_Dflag == TRUE)
fill_spec(i); fill_spec(i);
if ((j == nmix) && (stag_data->count_stag == 0 || i == 0 if ((j == nmix) && (stag_data->count_stag == 0 || i == 0
|| (i != 1 + count_cells && Utilities::Rxn_find(Rxn_solution_map, i + 1 + count_cells) == 0))) || (i != 1 + count_cells && Utilities::Rxn_find(Rxn_solution_map, i + 1 + count_cells) == 0)))
@ -1624,7 +1624,7 @@ fill_spec(int l_cell_no)
struct master *master_ptr; struct master *master_ptr;
LDBLE dum, dum2; LDBLE dum, dum2;
LDBLE lm; LDBLE lm;
LDBLE por, por_il, viscos_f, viscos_il_f, viscos; LDBLE por, por_il, viscos_f, viscos_il_f, viscos, l_z, l_g, ff;
bool x_max_done = false; bool x_max_done = false;
s_ptr2 = NULL; s_ptr2 = NULL;
@ -1813,6 +1813,20 @@ fill_spec(int l_cell_no)
else else
sol_D[l_cell_no].spec[count_spec].Dwt = s_ptr->dw * viscos_f; sol_D[l_cell_no].spec[count_spec].Dwt = s_ptr->dw * viscos_f;
} }
if (correct_Dw)
{
if ((l_z = fabs(s_x[i]->z)) == 0)
{ // first approximation for neutral species (HTO), but is viscosity dependent
l_z = 1;
l_g = -DH_A * (sqrt(mu_x) / (1 + sqrt(mu_x)));
}
else
l_g = s_ptr->lg;
ff = (mu_x < .36 * l_z ? 0.6 / sqrt(l_z) : sqrt(mu_x) / l_z);
ff *= l_g;
if (ff > 0) ff = 0; // is viscosity dependent (ff > 0 in KCl)
sol_D[l_cell_no].spec[count_spec].Dwt *= under(ff);
}
if (sol_D[l_cell_no].spec[count_spec].Dwt * pow(por, multi_Dn) > diffc_max) if (sol_D[l_cell_no].spec[count_spec].Dwt * pow(por, multi_Dn) > diffc_max)
diffc_max = sol_D[l_cell_no].spec[count_spec].Dwt * pow(por, multi_Dn); diffc_max = sol_D[l_cell_no].spec[count_spec].Dwt * pow(por, multi_Dn);
sol_D[l_cell_no].spec[count_spec].erm_ddl = s_ptr->erm_ddl; sol_D[l_cell_no].spec[count_spec].erm_ddl = s_ptr->erm_ddl;